{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_selection = \"cDNA\" and tissue_curation = \"Liver\"", "rows": [[171, "DRR075399", "DRX069313", "DRS075494", "DRP004473", "PRJDB5226", "Effects of local gut tumor on whole organismal gene expressions in zebrafish", "DRP004473", "Other", "How tumors affects whole organismal physiology remains largely unknown. To address this  we established the novel gut tumor model in zebrafish  Danio rerio. This model develops tumor at an early stage of juvenile development  when zebrafish larvae are small <4mm  enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver  the gut/gut tumor  and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor  contributing to discovering novel tumor organ interactions and their mediators in zebrafish.", null, null, "The liver of control fish 7dpf", "Control liver", "SAMD00065413", null, "sample name:3 control liver 150701 Hiseq3A l3 019|tissue type:Liver", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00065413", "DRX069313", "Control liver", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP004473", "Illumina HiSeq 2500 sequencing of SAMD00065413", null, null, null, 951579036.0, 26432751.0, "DRR075399", "0:36", "A:231570583;C:228182815;G:227223430;T:264569214;N:32994", 36, null, null, null, 231570583, 228182815, 227223430, 264569214, 32994, "DRX069313", "DRS075494", "DRA005199", "ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", "The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", 1, 0.8903, null, 0.08667, null, 0.7236, null, 0.51557, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2018-09-19", "Larval", "Larval", "Liver", "Liver and Biliary System"], [8104, "ERR2455366", "ERX2474426", "ERS2327331", "ERP107743", "PRJEB25789", "RNA seq of zebrafish larvae fed with different diets", "E-MTAB-6636", "Transcriptome Analysis", "We aim to establish NAFLD model of Zebrafish.  Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29", null, "Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Sample 4", "SAMEA104725948", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College", "ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725948|INSDC center name:Institute of Medicinal Biotechnology  Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 4|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:overfeeding|organism part:liver|sample name:E MTAB 6636:Sample 4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "E MTAB 6636:Sample 4 s", "Sample 4 s", "RNA seq of zebrafish larvae fed with different diets", "Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB.   Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Experimental Factor: diet:overfeeding", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP107743", "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16", "OF-4_H7MWNALXX_L6_1.fq.gz", "fastq", 4961276550.0, 33075177.0, "E MTAB 6636:Sample 4", "0:150 1:0", "A:1349413168;C:1135314970;G:1137935563;T:1338034716;N:578133", 150, 0, null, null, 1349413168, 1135314970, 1137935563, 1338034716, 578133, "ERX2474426", "ERS2327331", "ERA1259907", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", 1, 0.90787, null, 0.11999, null, 0.66123, null, 0.49072, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-03-29", "Larval", "Larval", "Liver", "Liver and Biliary System"], [8105, "ERR2455365", "ERX2474425", "ERS2327330", "ERP107743", "PRJEB25789", "RNA seq of zebrafish larvae fed with different diets", "E-MTAB-6636", "Transcriptome Analysis", "We aim to establish NAFLD model of Zebrafish.  Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29", null, "Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Sample 3", "SAMEA104725947", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College", "ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725947|INSDC center name:Institute of Medicinal Biotechnology  Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:fructose|organism part:liver|sample name:E MTAB 6636:Sample 3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "E MTAB 6636:Sample 3 s", "Sample 3 s", "RNA seq of zebrafish larvae fed with different diets", "Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB.   Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Experimental Factor: diet:fructose", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP107743", "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16", "Fru-3_H7MWNALXX_L5_1.fq.gz", "fastq", 5858273250.0, 39055155.0, "E MTAB 6636:Sample 3", "0:150 1:0", "A:1580150663;C:1353221682;G:1355865524;T:1568428138;N:607243", 150, 0, null, null, 1580150663, 1353221682, 1355865524, 1568428138, 607243, "ERX2474425", "ERS2327330", "ERA1259907", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", 1, 0.91505, null, 0.11036, null, 0.65985, null, 0.48443, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-03-29", "Larval", "Larval", "Liver", "Liver and Biliary System"], [8106, "ERR2455364", "ERX2474424", "ERS2327329", "ERP107743", "PRJEB25789", "RNA seq of zebrafish larvae fed with different diets", "E-MTAB-6636", "Transcriptome Analysis", "We aim to establish NAFLD model of Zebrafish.  Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29", null, "Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Sample 2", "SAMEA104725946", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College", "ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725946|INSDC center name:Institute of Medicinal Biotechnology  Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:cholesterol|organism part:liver|sample name:E MTAB 6636:Sample 2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "E MTAB 6636:Sample 2 s", "Sample 2 s", "RNA seq of zebrafish larvae fed with different diets", "Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB.   Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Experimental Factor: diet:cholesterol", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP107743", "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16", "Cho-2_H7MWNALXX_L5_1.fq.gz", "fastq", 5636304900.0, 37575366.0, "E MTAB 6636:Sample 2", "0:150 1:0", "A:1526862069;C:1295343770;G:1298751994;T:1514766898;N:580169", 150, 0, null, null, 1526862069, 1295343770, 1298751994, 1514766898, 580169, "ERX2474424", "ERS2327329", "ERA1259907", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", 1, 0.91032, null, 0.11644, null, 0.66649, null, 0.47766, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-03-29", "Larval", "Larval", "Liver", "Liver and Biliary System"], [8107, "ERR2455363", "ERX2474423", "ERS2327328", "ERP107743", "PRJEB25789", "RNA seq of zebrafish larvae fed with different diets", "E-MTAB-6636", "Transcriptome Analysis", "We aim to establish NAFLD model of Zebrafish.  Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29", null, "Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Sample 1", "SAMEA104725945", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College", "ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725945|INSDC center name:Institute of Medicinal Biotechnology  Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:control|organism part:liver|sample name:E MTAB 6636:Sample 1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "E MTAB 6636:Sample 1 s", "Sample 1 s", "RNA seq of zebrafish larvae fed with different diets", "Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB.   Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB  USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Experimental Factor: diet:control", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP107743", "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16", "ND-1_H7MWNALXX_L5_1.fq.gz", "fastq", 5197165350.0, 34647769.0, "E MTAB 6636:Sample 1", "0:150 1:0", "A:1430911816;C:1174811274;G:1175616551;T:1415284019;N:541690", 150, 0, null, null, 1430911816, 1174811274, 1175616551, 1415284019, 541690, "ERX2474423", "ERS2327328", "ERA1259907", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", 1, 0.89838, null, 0.13883, null, 0.66129, null, 0.48467, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-03-29", "Larval", "Larval", "Liver", "Liver and Biliary System"], [34958, "SRR32588715", "SRX27895236", "SRS24266238", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 F L22", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from liver", "C2 F2 F L22", "C2 F2 F L22", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m64467e_240816_172726.hifi_reads.flnc.fastq.gz", "fastq", 15103018596.0, 3471157.0, "m64467e 240816 172726.hifi reads.flnc.fastq.gz", "0:4351.00", "A:4102928612;C:3526979790;G:3455927740;T:4017182454;N:0", 4351, null, null, null, 4102928612, 3526979790, 3455927740, 4017182454, 0, "SRX27895236", "SRS24266238", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Adult", "Adult", "Liver", "Liver and Biliary System"], [34959, "SRR32588716", "SRX27895235", "SRS24266237", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 F L21", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:Liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from liver", "C2 F2 F L21", "C2 F2 F L21", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m84270_240913_130745_s1.skera.flnc.fastq.gz", "fastq", 91129501236.0, 45094963.0, "m84270 240913 130745 s1.skera.flnc.fastq.gz", "0:2020.84", "A:25808290124;C:20578070676;G:20740793271;T:24002347165;N:0", 2020, null, null, null, 25808290124, 20578070676, 20740793271, 24002347165, 0, "SRX27895235", "SRS24266237", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Adult", "Adult", "Liver", "Liver and Biliary System"], [34969, "SRR32588726", "SRX27895225", "SRS24266223", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 M L", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from liver", "C2 F2 M L", "C2 F2 M L", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m84270_240911_170652_s2.skera.flnc.fastq.gz", "fastq", 103288926144.0, 58528654.0, "m84270 240911 170652 s2.skera.flnc.fastq.gz", "0:1764.76", "A:30548263427;C:22289732504;G:23327561779;T:27123368434;N:0", 1764, null, null, null, 30548263427, 22289732504, 23327561779, 27123368434, 0, "SRX27895225", "SRS24266223", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Adult", "Adult", "Liver", "Liver and Biliary System"], [36336, "SRR390721", "SRX112005", "SRS282726", "SRP009863", "PRJNA151317", "A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver", "GSE34493", "Transcriptome Analysis", "We sequenced mRNA from each transgenic zebrafish line including WT  HBx  HCP  and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.", null, null, null, "mRNA from HBx+HCP transgenic line", "GSM850201", null, "source name:zebrafish liver|phenotype:intrahepatic cholangiocarcinoma|strain:HBx+HCP transgenic|tissue:liver", "mRNA from HBx+HCP transgenic line", "HBx+HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.", "zebrafish liver", "Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis", "The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing  the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation  the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.", "Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 \u00b0C.", "phenotype:intrahepatic cholangiocarcinoma|strain:HBx+HCP transgenic|tissue:liver", "GSM850201", "GSM850201: mRNA from HBx+HCP transgenic line; Danio rerio; RNA Seq", "GSM850201 1", "GSM850201: mRNA from HBx+HCP transgenic line", "1", null, "GEO Accession:GSM850201", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP009863", null, null, "HBx+HCP.qual HBx+HCP.csfasta", "SOLiD_native SOLiD_native", 3946087000.0, 78921740.0, "GSM850201 r1", "0:50", "0:926148003;1:1112848138;2:1139608445;3:763770020;.:3712394", 50, null, null, null, null, null, null, null, null, "SRX112005", "SRS282726", "SRA048698", "GEO", "Institute of Cellular and Organismic Biology, Academia Sinica", 1, 0.71816, null, 0.05681, null, 0.91727, null, 0.25279, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Taiwan", "2011-12-16", "Undetermined", "Adult", "Liver", "Liver and Biliary System"], [36337, "SRR390720", "SRX112004", "SRS282725", "SRP009863", "PRJNA151317", "A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver", "GSE34493", "Transcriptome Analysis", "We sequenced mRNA from each transgenic zebrafish line including WT  HBx  HCP  and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.", null, null, null, "mRNA from HCP transgenic line", "GSM850200", null, "source name:zebrafish liver|phenotype:n1|strain:HCP transgenic|tissue:liver", "mRNA from HCP transgenic line", "HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.", "zebrafish liver", "Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis", "The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing  the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation  the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.", "Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 \u00b0C.", "phenotype:n1|strain:HCP transgenic|tissue:liver", "GSM850200", "GSM850200: mRNA from HCP transgenic line; Danio rerio; RNA Seq", "GSM850200 1", "GSM850200: mRNA from HCP transgenic line", "1", null, "GEO Accession:GSM850200", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP009863", null, null, "HCP.qual HCP.csfasta", "SOLiD_native SOLiD_native", 4104044600.0, 82080892.0, "GSM850200 r1", "0:50", "0:944238890;1:1172273582;2:1207771613;3:775967445;.:3793070", 50, null, null, null, null, null, null, null, null, "SRX112004", "SRS282725", "SRA048698", "GEO", "Institute of Cellular and Organismic Biology, Academia Sinica", 1, 0.70132, null, 0.05286, null, 0.94422, null, 0.26785, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Taiwan", "2011-12-16", "Undetermined", "Adult", "Liver", "Liver and Biliary System"], [36338, "SRR390719", "SRX112003", "SRS282724", "SRP009863", "PRJNA151317", "A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver", "GSE34493", "Transcriptome Analysis", "We sequenced mRNA from each transgenic zebrafish line including WT  HBx  HCP  and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.", null, null, null, "mRNA from HBx transgenic line", "GSM850199", null, "source name:zebrafish liver|phenotype:n1|strain:HBx transgenic|tissue:liver", "mRNA from HBx transgenic line", "HBx count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.", "zebrafish liver", "Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis", "The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing  the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation  the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.", "Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 \u00b0C.", "phenotype:n1|strain:HBx transgenic|tissue:liver", "GSM850199", "GSM850199: mRNA from HBx transgenic line; Danio rerio; RNA Seq", "GSM850199 1", "GSM850199: mRNA from HBx transgenic line", "1", null, "GEO Accession:GSM850199", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP009863", null, null, "HBx.qual HBx.csfasta", "SOLiD_native SOLiD_native", 3783924950.0, 75678499.0, "GSM850199 r1", "0:50", "0:909506019;1:1055965468;2:1075994223;3:739008253;.:3450987", 50, null, null, null, null, null, null, null, null, "SRX112003", "SRS282724", "SRA048698", "GEO", "Institute of Cellular and Organismic Biology, Academia Sinica", 1, 0.70675, null, 0.04174, null, 0.94146, null, 0.22954, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Taiwan", "2011-12-16", "Undetermined", "Adult", "Liver", "Liver and Biliary System"], [36339, "SRR390718", "SRX112002", "SRS282723", "SRP009863", "PRJNA151317", "A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver", "GSE34493", "Transcriptome Analysis", "We sequenced mRNA from each transgenic zebrafish line including WT  HBx  HCP  and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.", null, null, null, "mRNA from AB strain", "GSM850198", null, "source name:zebrafish liver|phenotype:n1|strain:AB|tissue:liver", "mRNA from AB strain", "WT count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.", "zebrafish liver", "Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis", "The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing  the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation  the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.", "Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 \u00b0C.", "phenotype:n1|strain:AB|tissue:liver", "GSM850198", "GSM850198: mRNA from AB strain; Danio rerio; RNA Seq", "GSM850198 1", "GSM850198: mRNA from AB strain", "1", null, "GEO Accession:GSM850198", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP009863", null, null, "WT.csfasta WT.qual", "SOLiD_native SOLiD_native", 5129652800.0, 102593056.0, "GSM850198 r1", "0:50", "0:1167298346;1:1421158274;2:1551481320;3:984758434;.:4956426", 50, null, null, null, null, null, null, null, null, "SRX112002", "SRS282723", "SRA048698", "GEO", "Institute of Cellular and Organismic Biology, Academia Sinica", 1, 0.73072, null, 0.04843, null, 0.95574, null, 0.21796, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Taiwan", "2011-12-16", "Undetermined", "Adult", "Liver", "Liver and Biliary System"], [36506, "SRR566696", "SRX185761", "SRS361914", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: liver tumor  M+D+", "GSM1000561: M+D+ 2", "GSM1000561", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline", "M+D+ 2", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "liver tumor  M+D+", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline", "GSM1000561", "GSM1000561: M+D+ 2; Danio rerio; RNA Seq", "GSM1000561 1", null, "1", null, "GEO Accession:GSM1000561", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M+D+_2_QV.qual M+D+_2.csfasta", "SOLiD_native SOLiD_native", 1493416960.0, 42669056.0, "GSM1000561 r1", "0:35", "0:377247910;1:348861020;2:522134600;3:237405266;.:7768164", 35, null, null, null, null, null, null, null, null, "SRX185761", "SRS361914", "SRA058618", "GEO", "National University of Singapore", 1, 0.06244, null, 0.00306, null, 0.99567, null, 0.34618, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36507, "SRR566695", "SRX185760", "SRS361913", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: liver tumor  M+D+", "GSM1000560: M+D+ 1", "GSM1000560", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline", "M+D+ 1", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "liver tumor  M+D+", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline", "GSM1000560", "GSM1000560: M+D+ 1; Danio rerio; RNA Seq", "GSM1000560 1", null, "1", null, "GEO Accession:GSM1000560", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, null, null, 1291539515.0, 36901129.0, "GSM1000560 r1", "0:35", "0:266006021;1:328523841;2:440474617;3:254266912;.:2268124", 35, null, null, null, null, null, null, null, null, "SRX185760", "SRS361913", "SRA058618", "GEO", "National University of Singapore", 1, 0.10629, null, 0.0044, null, 0.99239, null, 0.31953, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36508, "SRR566694", "SRX185759", "SRS361912", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M D+", "GSM1000559: M D+ 2", "GSM1000559", null, "genotype:wildtype|tissue:liver|treatment:doxycycline", "M D+ 2", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M D+", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:wildtype|tissue:liver|treatment:doxycycline", "GSM1000559", "GSM1000559: M D+ 2; Danio rerio; RNA Seq", "GSM1000559 1", null, "1", null, "GEO Accession:GSM1000559", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M-D+_2_QV.qual", "SOLiD_native", 1438423910.0, 41097826.0, "GSM1000559 r1", "0:35", "0:353104627;1:349496969;2:433338629;3:275089557;.:27394128", 35, null, null, null, null, null, null, null, null, "SRX185759", "SRS361912", "SRA058618", "GEO", "National University of Singapore", 1, 0.04748, null, 0.00442, null, 0.99425, null, 0.53794, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36509, "SRR566693", "SRX185758", "SRS361911", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M D+", "GSM1000558: M D+ 1", "GSM1000558", null, "genotype:wildtype|tissue:liver|treatment:doxycycline", "M D+ 1", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M D+", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:wildtype|tissue:liver|treatment:doxycycline", "GSM1000558", "GSM1000558: M D+ 1; Danio rerio; RNA Seq", "GSM1000558 1", null, "1", null, "GEO Accession:GSM1000558", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M-D+_1.csfasta", "SOLiD_native", 1284638285.0, 36703951.0, "GSM1000558 r1", "0:35", "0:328871758;1:317693850;2:402981931;3:233637468;.:1453278", 35, null, null, null, null, null, null, null, null, "SRX185758", "SRS361911", "SRA058618", "GEO", "National University of Singapore", 1, 0.10539, null, 0.00562, null, 0.99141, null, 0.37635, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36510, "SRR566692", "SRX185757", "SRS361910", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M+D ", "GSM1000557: M+D  2", "GSM1000557", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1", "M+D  2", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M+D ", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1", "GSM1000557", "GSM1000557: M+D  2; Danio rerio; RNA Seq", "GSM1000557 1", null, "1", null, "GEO Accession:GSM1000557", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M+D-_2_QV.qual", "SOLiD_native", 1404966080.0, 40141888.0, "GSM1000557 r1", "0:35", "0:371691603;1:354481639;2:405221861;3:271978812;.:1592165", 35, null, null, null, null, null, null, null, null, "SRX185757", "SRS361910", "SRA058618", "GEO", "National University of Singapore", 1, 0.07869, null, 0.00455, null, 0.99253, null, 0.51508, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36511, "SRR566691", "SRX185756", "SRS361909", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M+D ", "GSM1000556: M+D  1", "GSM1000556", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1", "M+D  1", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M+D ", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1", "GSM1000556", "GSM1000556: M+D  1; Danio rerio; RNA Seq", "GSM1000556 1", null, "1", null, "GEO Accession:GSM1000556", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M+D-_1_QV.qual M+D-_1.csfasta", "SOLiD_native SOLiD_native", 1286706820.0, 36763052.0, "GSM1000556 r1", "0:35", "0:252864341;1:338709089;2:436928155;3:256235022;.:1970213", 35, null, null, null, null, null, null, null, null, "SRX185756", "SRS361909", "SRA058618", "GEO", "National University of Singapore", 1, 0.12399, null, 0.00617, null, 0.98752, null, 0.50351, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36512, "SRR566690", "SRX185755", "SRS361908", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M D ", "GSM1000555: M D  2", "GSM1000555", null, "genotype:wildtype|tissue:liver|treatment:n1", "M D  2", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M D ", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:wildtype|tissue:liver|treatment:n1", "GSM1000555", "GSM1000555: M D  2; Danio rerio; RNA Seq", "GSM1000555 1", null, "1", null, "GEO Accession:GSM1000555", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M-D-_2_QV.qual M-D-_2.csfasta", "SOLiD_native SOLiD_native", 1337952770.0, 38227222.0, "GSM1000555 r1", "0:35", "0:391863829;1:347720340;2:312814682;3:283542736;.:2011183", 35, null, null, null, null, null, null, null, null, "SRX185755", "SRS361908", "SRA058618", "GEO", "National University of Singapore", 1, 0.04605, null, 0.00365, null, 0.99494, null, 0.51825, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36513, "SRR566689", "SRX185754", "SRS361907", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus  our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D   M+D   M D+ were generated by deep sequencing  each in duplicates  using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver  M D ", "GSM1000554: M D  1", "GSM1000554", null, "genotype:wildtype|tissue:liver|treatment:n1", "M D  1", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver  M D ", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:wildtype|tissue:liver|treatment:n1", "GSM1000554", "GSM1000554: M D  1; Danio rerio; RNA Seq", "GSM1000554 1", null, "1", null, "GEO Accession:GSM1000554", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M-D-_1.csfasta", "SOLiD_native", 1395143680.0, 39861248.0, "GSM1000554 r1", "0:35", "0:439852883;1:355203725;2:298639546;3:299770820;.:1676706", 35, null, null, null, null, null, null, null, null, "SRX185754", "SRS361907", "SRA058618", "GEO", "National University of Singapore", 1, 0.02094, null, 0.00123, null, 0.99784, null, 0.58426, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [37108, "SRR924082", "SRX316721", "SRS472258", "SRP026400", "PRJNA210007", "Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver", "GSE48427", "Transcriptome Analysis", "In the present study  we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure  including oxidation reduction  translation  iron ion transport  cell redox and homeostasis  as well as related pathways in metabolism and diseases. Furthermore  as there are currently no biomarker genes available for predicting arsenic exposure  we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system.", null, "pubmed:24176670;pubmed:23922661", null, "H2O treated zebrafish liver", "GSM1177837", null, "source name:liver  control|genotype/variation:wildtype|tissue:liver|age:3 month|treatment:water control", "H2O treated zebrafish liver", "The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI  RefSeq accession  and expression levels in TPM.", "liver  control", "3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day.", "Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype/variation:wildtype|tissue:liver|age:3 month|treatment:water control", "GSM1177837", "GSM1177837: H2O treated zebrafish liver; Danio rerio; RNA Seq", "GSM1177837", null, "1", "Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", "GEO Accession:GSM1177837", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP026400", null, null, "solid0518_20101014_Gong_1_SetA_F3_0_1H2O.csfasta solid0518_20101014_Gong_1_SetA_F3_QV_0_1H2O.qual", "SOLiD_native SOLiD_native", 477311205.0, 13637463.0, "GSM1177837 r1", "0:35", "0:176467601;1:101093405;2:105775125;3:93265462;.:709612", 35, null, null, null, null, null, null, null, null, "SRX316721", "SRS472258", "SRA091803", "GEO", "National University of Singapore", 1, 0.02019, null, 0.01385, null, 0.9973, null, 0.64062, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-06-28", "Adult", "Adult", "Liver", "Liver and Biliary System"], [37109, "SRR924081", "SRX316720", "SRS454027", "SRP026400", "PRJNA210007", "Genome wide identification of molecular pathways and biomarkers in response to arsenic exposure in zebrafish liver", "GSE48427", "Transcriptome Analysis", "In the present study  we employed the RNA sequencing platform to examine the molecular response of zebrafish liver to arsenic exposure and carry out detailed transcriptomic analyses for further understanding of molecular toxicity. We found that several important biological processes were perturbed by arsenic exposure  including oxidation reduction  translation  iron ion transport  cell redox and homeostasis  as well as related pathways in metabolism and diseases. Furthermore  as there are currently no biomarker genes available for predicting arsenic exposure  we took the advantage of RNA sequencing platform to identify most suitable biomarker genes from top responsive genes to arsenic exposure. We first validated these top responsive genes by RT qPCR in zebrafish and then in Japanese medaka Oryzias latipes at individual fish level for more robustly responsive genes across different fish species. Overall design: Transcriptome profiling of arsenic treated sample and control sample were generated by deep sequencing using three prime RNA SAGE on the SOLiD system.", null, "pubmed:24176670;pubmed:23922661", null, "Arsenic treated zebrafish liver", "GSM1177836", null, "source name:liver  arsenic|genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium", "Arsenic treated zebrafish liver", "The SOLiD generated RNA Seq reads were 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maximum mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 58 Supplementary files format and content: Tab delimited text file. The mapped transcripts are listed with GI  RefSeq accession  and expression levels in TPM.", "liver  arsenic", "3 mpf wildtype zebrafish were treated for 96 hrs. Sodium arsenate treatment was conducted in 3 L tanks with around 15 adults and water was changed every day.", "Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype/variation:wildtype|tissue:liver|age:3 month|treatment:arsenate sodium", "GSM1177836", "GSM1177836: Arsenic treated zebrafish liver; Danio rerio; RNA Seq", "GSM1177836", null, "1", "Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", "GEO Accession:GSM1177836", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP026400", null, null, "solid0518_20101014_Gong_1_SetA_F3_QV_2_2Arsenic.qual solid0518_20101014_Gong_1_SetA_F3_2_2Arsenic.csfasta", "SOLiD_native SOLiD_native", 477279215.0, 13636549.0, "GSM1177836 r1", "0:35", "0:135280436;1:121477647;2:102046207;3:117826846;.:648079", 35, null, null, null, null, null, null, null, null, "SRX316720", "SRS454027", "SRA091803", "GEO", "National University of Singapore", 1, 0.0161, null, 0.00302, null, 0.99334, null, 0.51629, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-06-28", "Adult", "Adult", "Liver", "Liver and Biliary System"], [37130, "SRR952910", "SRX335554", "SRS470625", "SRP028848", "PRJNA215326", "Transcriptomic analyses of TCDD treated zebrafish liver", "GSE49915", "Transcriptome Analysis", "To fully understand molecular toxicity of TCDD in an in vivo animal model  adult zebrafish were exposed to TCDD at xxx nM for xxx h and the livers were sampled for RNA sequencing based transcriptomic profiling. A total of 1 058 differently expressed genes were identified based on fold change>2 and TPM transcripts per million >10. Among the top 20 up regulated genes  10 novel responsive genes were identified and verified by qRT PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle  endocrine disruptors  signal transduction and immune systems. Comparative analyses of TCDD induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up regulated while calcium signaling pathway and several immune related pathways are generally down regulated. Overall design: Transcriptome profiling of treated sample TCDD and control sample DMSO were generated by deep sequencing using three prime RNA SAGE with SOLiD system", null, "pubmed:24204792", null, "DMSO", "GSM1209643", null, "source name:liver|tissue:liver|genotype:wildtype sibling|treatment:DMSO", "DMSO", "The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Supplementary files format and content: The mapped transcripts were listed with GI and expression levels in TPM.", "liver", "3 mpf wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3 L tanks with around 15 adult and water was changed every day.", "Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", null, "tissue:liver|genotype:wildtype sibling|treatment:DMSO", "GSM1209643", "GSM1209643: DMSO; Danio rerio; RNA Seq", "GSM1209643", null, "1", "Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", "GEO Accession:GSM1209643", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP028848", null, null, "solid0518_20101014_Gong_1_SetA_F3_0_2DMSO.csfasta solid0518_20101014_Gong_1_SetA_F3_QV_0_2DMSO.qual", "SOLiD_native SOLiD_native", 409327205.0, 11695063.0, "GSM1209643 r1", "0:35", "0:136723730;1:95263220;2:87949986;3:88818989;.:571280", 35, null, null, null, null, null, null, null, null, "SRX335554", "SRS470625", "SRA098000", "GEO", "National University of Singapore", 1, 0.01735, null, 0.00647, null, 0.9946, null, 0.51324, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-08-15", "Adult", "Adult", "Liver", "Liver and Biliary System"], [37131, "SRR952909", "SRX335553", "SRS470624", "SRP028848", "PRJNA215326", "Transcriptomic analyses of TCDD treated zebrafish liver", "GSE49915", "Transcriptome Analysis", "To fully understand molecular toxicity of TCDD in an in vivo animal model  adult zebrafish were exposed to TCDD at xxx nM for xxx h and the livers were sampled for RNA sequencing based transcriptomic profiling. A total of 1 058 differently expressed genes were identified based on fold change>2 and TPM transcripts per million >10. Among the top 20 up regulated genes  10 novel responsive genes were identified and verified by qRT PCR analysis on independent samples. Transcriptomic analysis indicated several deregulated pathways associated with cell cycle  endocrine disruptors  signal transduction and immune systems. Comparative analyses of TCDD induced transcriptomic changes between fish and mammalian models revealed that proteomic pathway is consistently up regulated while calcium signaling pathway and several immune related pathways are generally down regulated. Overall design: Transcriptome profiling of treated sample TCDD and control sample DMSO were generated by deep sequencing using three prime RNA SAGE with SOLiD system", null, "pubmed:24204792", null, "TCDD", "GSM1209642", null, "source name:liver|tissue:liver|genotype:wildtype sibling|treatment:TCDD", "TCDD", "The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Supplementary files format and content: The mapped transcripts were listed with GI and expression levels in TPM.", "liver", "3 mpf wildtype zebrafish were treated for 96 hrs. TCDD or DMSO treatment was conducted in 3 L tanks with around 15 adult and water was changed every day.", "Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", null, "tissue:liver|genotype:wildtype sibling|treatment:TCDD", "GSM1209642", "GSM1209642: TCDD; Danio rerio; RNA Seq", "GSM1209642", null, "1", "Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", "GEO Accession:GSM1209642", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP028848", null, null, "solid0518_20101014_Gong_1_SetA_F3_QV_1_2TCDD.qual solid0518_20101014_Gong_1_SetA_F3_1_2TCDD.csfasta", "SOLiD_native SOLiD_native", 627514895.0, 17928997.0, "GSM1209642 r1", "0:35", "0:214639659;1:142538233;2:131819822;3:137625000;.:892181", 35, null, null, null, null, null, null, null, null, "SRX335553", "SRS470624", "SRA098000", "GEO", "National University of Singapore", 1, 0.01773, null, 0.00917, null, 0.99646, null, 0.56398, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-08-15", "Adult", "Adult", "Liver", "Liver and Biliary System"], [37217, "SRR1035240", "SRX381137", "SRS505529", "SRP033231", "PRJNA229468", "Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma", "GSE52605", "Transcriptome Analysis", "UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish  cultured cells and human tumors  we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Overall design: Total small RNA from 2 batches of Tgfabp10:has.UHRF1 GFPHigh and age matched Tgfabp10:nls mCherry control 5 dpf zebrafish livers was purified for preparation of high throughput sequencing libraries.", null, "pubmed:24486181", null, "mCherry cntr2", "GSM1272461", null, "source name:Zebrafish 5 dpf liver|genotype/variation:Tgfabp10:nls mCherry|tissue:liver|development stage:5 dpf", "mCherry cntr2", "Illumina CASAVA version 1.7 used for basecalling Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al.  2008; Olson et al.  2008; Tam et al.  2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes genes and their quantile normalized frequencies.", "Zebrafish 5 dpf liver", null, "Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.", null, "genotype/variation:Tgfabp10:nls mCherry|tissue:liver|developmental stage:5 dpf", "GSM1272461", "GSM1272461: mCherry cntr2; Danio rerio; RNA Seq", "GSM1272461", null, "1", "Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.", "GEO Accession:GSM1272461", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP033231", null, null, "mCherry_cntr2.fastq.gz", "fastq", 2132003100.0, 21320031.0, "GSM1272461 r1", "0:100", "A:536532013;C:533562250;G:522685362;T:536641910;N:2581565", 100, null, null, null, 536532013, 533562250, 522685362, 536641910, 2581565, "SRX381137", "SRS505529", "SRA111986", "GEO", "sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai", 1, 0.88347, null, 0.04357, null, 0.81964, null, 0.52384, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-11-21", "Larval", "Larval", "Liver", "Liver and Biliary System"], [37218, "SRR1035239", "SRX381136", "SRS505528", "SRP033231", "PRJNA229468", "Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma", "GSE52605", "Transcriptome Analysis", "UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish  cultured cells and human tumors  we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Overall design: Total small RNA from 2 batches of Tgfabp10:has.UHRF1 GFPHigh and age matched Tgfabp10:nls mCherry control 5 dpf zebrafish livers was purified for preparation of high throughput sequencing libraries.", null, "pubmed:24486181", null, "mCherry cntr1", "GSM1272460", null, "source name:Zebrafish 5 dpf liver|genotype/variation:Tgfabp10:nls mCherry|tissue:liver|development stage:5 dpf", "mCherry cntr1", "Illumina CASAVA version 1.7 used for basecalling Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al.  2008; Olson et al.  2008; Tam et al.  2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes genes and their quantile normalized frequencies.", "Zebrafish 5 dpf liver", null, "Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.", null, "genotype/variation:Tgfabp10:nls mCherry|tissue:liver|developmental stage:5 dpf", "GSM1272460", "GSM1272460: mCherry cntr1; Danio rerio; RNA Seq", "GSM1272460", null, "1", "Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.", "GEO Accession:GSM1272460", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP033231", null, null, "mCherry_cntr1.fastq.gz", "fastq", 2098395500.0, 20983955.0, "GSM1272460 r1", "0:100", "A:533756912;C:521877600;G:512200617;T:528020965;N:2539406", 100, null, null, null, 533756912, 521877600, 512200617, 528020965, 2539406, "SRX381136", "SRS505528", "SRA111986", "GEO", "sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai", 1, 0.89445, null, 0.02866, null, 0.82426, null, 0.50861, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-11-21", "Larval", "Larval", "Liver", "Liver and Biliary System"], [37219, "SRR1035238", "SRX381135", "SRS505527", "SRP033231", "PRJNA229468", "Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma", "GSE52605", "Transcriptome Analysis", "UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish  cultured cells and human tumors  we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Overall design: Total small RNA from 2 batches of Tgfabp10:has.UHRF1 GFPHigh and age matched Tgfabp10:nls mCherry control 5 dpf zebrafish livers was purified for preparation of high throughput sequencing libraries.", null, "pubmed:24486181", null, "UHRF1 hi B", "GSM1272459", null, "source name:Zebrafish 5 dpf liver|genotype/variation:Tgfabp10:has.UHRF1 GFP|tissue:liver|development stage:5 dpf", "UHRF1 hi B", "Illumina CASAVA version 1.7 used for basecalling Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al.  2008; Olson et al.  2008; Tam et al.  2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes genes and their quantile normalized frequencies.", "Zebrafish 5 dpf liver", null, "Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.", null, "genotype/variation:Tgfabp10:has.UHRF1 GFP|tissue:liver|developmental stage:5 dpf", "GSM1272459", "GSM1272459: UHRF1 hi B; Danio rerio; RNA Seq", "GSM1272459", null, "1", "Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.", "GEO Accession:GSM1272459", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP033231", null, null, "UHRF1_hi_B.fastq.gz", "fastq", 2127061900.0, 21270619.0, "GSM1272459 r1", "0:100", "A:540147604;C:542900044;G:522760277;T:518703604;N:2550371", 100, null, null, null, 540147604, 542900044, 522760277, 518703604, 2550371, "SRX381135", "SRS505527", "SRA111986", "GEO", "sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai", 1, 0.7609, null, 0.0395, null, 0.77788, null, 0.51544, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-11-21", "Larval", "Larval", "Liver", "Liver and Biliary System"], [37220, "SRR1035237", "SRX381134", "SRS505526", "SRP033231", "PRJNA229468", "Overexpression of UHRF1 drives DNA hypomethylation and hepatocellular carcinoma", "GSE52605", "Transcriptome Analysis", "UHRF1 is an essential regulator of DNA methylation that is highly expressed in many cancers. Using transgenic zebrafish  cultured cells and human tumors  we demonstrate that UHRF1 is an oncogene. RNAseq was used to assess the variation in gene expression between control and experimental samples. Overall design: Total small RNA from 2 batches of Tgfabp10:has.UHRF1 GFPHigh and age matched Tgfabp10:nls mCherry control 5 dpf zebrafish livers was purified for preparation of high throughput sequencing libraries.", null, "pubmed:24486181", null, "UHRF1 hi A", "GSM1272458", null, "source name:Zebrafish 5 dpf liver|genotype/variation:Tgfabp10:has.UHRF1 GFP|tissue:liver|development stage:5 dpf", "UHRF1 hi A", "Illumina CASAVA version 1.7 used for basecalling Mapped to the Danio rerio genome build Zv9/danRer7 Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non zero expression Values were quantile normalized allowing comparisons of the two sets using custom built software and algorithms as described Aravin et al.  2008; Olson et al.  2008; Tam et al.  2008 Genome build: Zv9/danRer7 Supplementary files format and content: Tab delimted text file includes genes and their quantile normalized frequencies.", "Zebrafish 5 dpf liver", null, "Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.", null, "genotype/variation:Tgfabp10:has.UHRF1 GFP|tissue:liver|developmental stage:5 dpf", "GSM1272458", "GSM1272458: UHRF1 hi A; Danio rerio; RNA Seq", "GSM1272458", null, "1", "Total RNA was extracted using Trizol and mRNA was purified using poly A beads The mRNA was chemically fragmented and Hi seq compatible  bar coded adapters were ligated to both ends.", "GEO Accession:GSM1272458", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP033231", null, null, "UHRF1_hi_A.fastq.gz", "fastq", 2476218900.0, 24762189.0, "GSM1272458 r1", "0:100", "A:625575890;C:631605318;G:620422311;T:595617894;N:2997487", 100, null, null, null, 625575890, 631605318, 620422311, 595617894, 2997487, "SRX381134", "SRS505526", "SRA111986", "GEO", "sachidanandam, Oncological Sciences, Icahn School of Medicine at Mount Sinai", 1, 0.80154, null, 0.04243, null, 0.80409, null, 0.50831, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-11-21", "Larval", "Larval", "Liver", "Liver and Biliary System"], [37271, "SRR1050719", "SRX392663", "SRS515660", "SRP034513", "PRJNA231764", "Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer", "GSE53342", "Transcriptome Analysis", "To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless  they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples  and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs  suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus  these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D   X M+D   X M D+  xmrk tumor sample X+M D+ and control samples X M D   X+M D   X M D+  were generated by deep sequencing  using three prime RNA SAGE on SOLiD system", null, "pubmed:24633177", null, "X+M D+", "GSM1289483", null, "source name:liver tumor|tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:doxycycline", "X+M D+", "The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "liver tumor", "Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", null, "tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:doxycycline", "GSM1289483", "GSM1289483: X+M D+; Danio rerio; RNA Seq", "GSM1289483", null, "1", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", "GEO Accession:GSM1289483", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP034513", null, null, "X+M-D+.csfasta.gz X+M-D+.qual", "SOLiD_native SOLiD_native", 367532585.0, 10500931.0, "GSM1289483 r1", "0:35", "0:113917936;1:90770860;2:74839037;3:87267038;.:737714", 35, null, null, null, null, null, null, null, null, "SRX392663", "SRS515660", "SRA117588", "GEO", "National University of Singapore", 1, 0.03142, null, 0.01041, null, 0.99115, null, 0.47722, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-12-16", "Adult", "Adult", "Liver", "Liver and Biliary System"], [37272, "SRR1050718", "SRX392662", "SRS515661", "SRP034513", "PRJNA231764", "Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer", "GSE53342", "Transcriptome Analysis", "To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless  they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples  and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs  suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus  these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D   X M+D   X M D+  xmrk tumor sample X+M D+ and control samples X M D   X+M D   X M D+  were generated by deep sequencing  using three prime RNA SAGE on SOLiD system", null, "pubmed:24633177", null, "X M+D+", "GSM1289482", null, "source name:liver tumor|tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:doxycycline", "X M+D+", "The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "liver tumor", "Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", null, "tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:doxycycline", "GSM1289482", "GSM1289482: X M+D+; Danio rerio; RNA Seq", "GSM1289482", null, "1", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", "GEO Accession:GSM1289482", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP034513", null, null, "X-M+D+.csfasta.gz X-M+D+.qual", "SOLiD_native SOLiD_native", 524940885.0, 14998311.0, "GSM1289482 r1", "0:35", "0:177873348;1:126792787;2:107434769;3:111636161;.:1203820", 35, null, null, null, null, null, null, null, null, "SRX392662", "SRS515661", "SRA117588", "GEO", "National University of Singapore", 1, 0.04433, null, 0.02519, null, 0.99456, null, 0.5443, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-12-16", "Adult", "Adult", "Liver", "Liver and Biliary System"], [37273, "SRR1050717", "SRX392661", "SRS515658", "SRP034513", "PRJNA231764", "Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer", "GSE53342", "Transcriptome Analysis", "To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless  they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples  and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs  suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus  these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D   X M+D   X M D+  xmrk tumor sample X+M D+ and control samples X M D   X+M D   X M D+  were generated by deep sequencing  using three prime RNA SAGE on SOLiD system", null, "pubmed:24633177", null, "X M D+", "GSM1289481", null, "source name:control liver|tissue:liver|genotype:wildtype sibling|agent:doxycycline", "X M D+", "The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver", "Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", null, "tissue:liver|genotype:wildtype sibling|agent:doxycycline", "GSM1289481", "GSM1289481: X M D+; Danio rerio; RNA Seq", "GSM1289481", null, "1", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", "GEO Accession:GSM1289481", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP034513", null, null, "X-M-D+.csfasta.gz X-M-D+.qual", "SOLiD_native SOLiD_native", 503677265.0, 14390779.0, "GSM1289481 r1", "0:35", "0:153190412;1:124381654;2:106372352;3:118615876;.:1116971", 35, null, null, null, null, null, null, null, null, "SRX392661", "SRS515658", "SRA117588", "GEO", "National University of Singapore", 1, 0.03136, null, 0.01201, null, 0.99356, null, 0.49598, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-12-16", "Adult", "Adult", "Liver", "Liver and Biliary System"], [37274, "SRR1050716", "SRX392660", "SRS515659", "SRP034513", "PRJNA231764", "Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer", "GSE53342", "Transcriptome Analysis", "To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless  they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples  and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs  suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus  these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D   X M+D   X M D+  xmrk tumor sample X+M D+ and control samples X M D   X+M D   X M D+  were generated by deep sequencing  using three prime RNA SAGE on SOLiD system", null, "pubmed:24633177", null, "X+M D ", "GSM1289480", null, "source name:control liver|tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:n1", "X+M D ", "The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver", "Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", null, "tissue:liver|genotype:Tgfabp10:TA; TRE:xmrk; krt4:GFP|agent:n1", "GSM1289480", "GSM1289480: X+M D ; Danio rerio; RNA Seq", "GSM1289480", null, "1", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", "GEO Accession:GSM1289480", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP034513", null, null, "X+M-D-.csfasta.gz X+M-D-.qual", "SOLiD_native SOLiD_native", 634523960.0, 18129256.0, "GSM1289480 r1", "0:35", "0:234010528;1:135057441;2:132344184;3:131577105;.:1534702", 35, null, null, null, null, null, null, null, null, "SRX392660", "SRS515659", "SRA117588", "GEO", "National University of Singapore", 1, 0.06814, null, 0.05142, null, 0.99579, null, 0.6174, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-12-16", "Adult", "Adult", "Liver", "Liver and Biliary System"], [37275, "SRR1050715", "SRX392659", "SRS515657", "SRP034513", "PRJNA231764", "Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer", "GSE53342", "Transcriptome Analysis", "To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless  they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples  and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs  suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus  these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D   X M+D   X M D+  xmrk tumor sample X+M D+ and control samples X M D   X+M D   X M D+  were generated by deep sequencing  using three prime RNA SAGE on SOLiD system", null, "pubmed:24633177", null, "X M+D ", "GSM1289479", null, "source name:control liver|tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:n1", "X M+D ", "The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver", "Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", null, "tissue:liver|genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|agent:n1", "GSM1289479", "GSM1289479: X M+D ; Danio rerio; RNA Seq", "GSM1289479", null, "1", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", "GEO Accession:GSM1289479", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP034513", null, null, "X-M+D-.csfasta.gz X-M+D-.qual", "SOLiD_native SOLiD_native", 417548565.0, 11929959.0, "GSM1289479 r1", "0:35", "0:114209112;1:103552786;2:91302789;3:107590004;.:893874", 35, null, null, null, null, null, null, null, null, "SRX392659", "SRS515657", "SRA117588", "GEO", "National University of Singapore", 1, 0.02253, null, 0.00519, null, 0.99218, null, 0.61466, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-12-16", "Adult", "Adult", "Liver", "Liver and Biliary System"], [37276, "SRR1050714", "SRX392658", "SRS515656", "SRP034513", "PRJNA231764", "Transcriptomic analyses of Myc and xmrk induced zebrafish liver cancer", "GSE53342", "Transcriptome Analysis", "To compare the characteristics and mechanisms of Myc and xmrk induced zebrafish liver tumor  next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that relatively small overlaps of significantly deregulated genes and biological pathways among different zebrafish liver tumor models.Nevertheless  they all significantly correlate with advanced or very advanced human hepatocellular carcinoma HCC. Molecular signature from each oncogene induced zebrafish liver tumor correlated with only a small subset of human HCC samples  and they share conserved up regulated pathways. A short list of commonly deregulated genes among different zebrafish liver tumors showed accordant deregulation in the majority of human HCCs  suggesting that they may serve as common diagnosis markers and therapeutic targets.Thus  these transgenic zebrafish models with well defined oncogene induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. Overall design: Transcriptome profiling of Myc tumor sample X M+D+ and control samples X M D   X M+D   X M D+  xmrk tumor sample X+M D+ and control samples X M D   X+M D   X M D+  were generated by deep sequencing  using three prime RNA SAGE on SOLiD system", null, "pubmed:24633177", null, "X M D ", "GSM1289478", null, "source name:control liver|tissue:liver|genotype:wildtype sibling|agent:n1", "X M D ", "The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver", "Transgenic zebrafish and their wildtype siblings were treated starting from 3.5 mpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adult and water was changed every other day.", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", null, "tissue:liver|genotype:wildtype sibling|agent:n1", "GSM1289478", "GSM1289478: X M D ; Danio rerio; RNA Seq", "GSM1289478", null, "1", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", "GEO Accession:GSM1289478", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP034513", null, null, "X-M-D-.csfasta.gz X-M-D-.qual", "SOLiD_native SOLiD_native", 522827305.0, 14937923.0, "GSM1289478 r1", "0:35", "0:143962506;1:130748449;2:106995057;3:140038917;.:1082376", 35, null, null, null, null, null, null, null, null, "SRX392658", "SRS515656", "SRA117588", "GEO", "National University of Singapore", 1, 0.02926, null, 0.00817, null, 0.99022, null, 0.53421, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-12-16", "Adult", "Adult", "Liver", "Liver and Biliary System"], [37277, "SRR1057959", "SRX398517", "SRS518969", "SRP034710", "PRJNA232516", "Transcriptomic analyses of Kras induced zebrafish liver cancer", "GSE53630", "Transcriptome Analysis", "The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing  using three prime' RNA SAGE on SOLiD system", null, "pubmed:24633177", null, "6T2", "GSM1297515", null, "source name:liver tumor|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis", "6T2", "The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "liver tumor", "one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", null, "tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis", "GSM1297515", "GSM1297515: 6T2; Danio rerio; RNA Seq", "GSM1297515", null, "1", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", "GEO Accession:GSM1297515", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP034710", null, null, "6T2.csfasta.gz 6T2.qual.gz", "SOLiD_native SOLiD_native", 818910190.0, 23397434.0, "GSM1297515 r1", "0:35", "0:347259734;1:164743259;2:162029194;3:130508344;.:14369659", 35, null, null, null, null, null, null, null, null, "SRX398517", "SRS518969", "SRA122333", "GEO", "National University of Singapore", 1, 0.03756, null, 0.0064, null, 0.99931, null, 0.92063, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-12-24", "Undetermined", "Adult", "Liver", "Liver and Biliary System"], [37278, "SRR1057958", "SRX398516", "SRS518968", "SRP034710", "PRJNA232516", "Transcriptomic analyses of Kras induced zebrafish liver cancer", "GSE53630", "Transcriptome Analysis", "The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing  using three prime' RNA SAGE on SOLiD system", null, "pubmed:24633177", null, "6T1", "GSM1297514", null, "source name:liver tumor|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis", "6T1", "The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "liver tumor", "one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", null, "tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis", "GSM1297514", "GSM1297514: 6T1; Danio rerio; RNA Seq", "GSM1297514", null, "1", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", "GEO Accession:GSM1297514", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP034710", null, null, "6T1.csfasta.gz 6T1.qual.gz", "SOLiD_native SOLiD_native", 761241005.0, 21749743.0, "GSM1297514 r1", "0:35", "0:306840116;1:164725874;2:160786359;3:126370697;.:2517959", 35, null, null, null, null, null, null, null, null, "SRX398516", "SRS518968", "SRA122333", "GEO", "National University of Singapore", 1, 0.0542, null, 0.00664, null, 0.99876, null, 0.95184, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-12-24", "Undetermined", "Adult", "Liver", "Liver and Biliary System"], [37279, "SRR1057957", "SRX398515", "SRS518967", "SRP034710", "PRJNA232516", "Transcriptomic analyses of Kras induced zebrafish liver cancer", "GSE53630", "Transcriptome Analysis", "The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing  using three prime' RNA SAGE on SOLiD system", null, "pubmed:24633177", null, "6M2", "GSM1297513", null, "source name:control liver|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control", "6M2", "The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver", "one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", null, "tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control", "GSM1297513", "GSM1297513: 6M2; Danio rerio; RNA Seq", "GSM1297513", null, "1", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", "GEO Accession:GSM1297513", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP034710", null, null, "6M2.csfasta.gz 6M2.qual.gz", "SOLiD_native SOLiD_native", 627546330.0, 20918211.0, "GSM1297513 r1", "0:30", "0:265606277;1:113800100;2:158432886;3:89099865;.:607202", 30, null, null, null, null, null, null, null, null, "SRX398515", "SRS518967", "SRA122333", "GEO", "National University of Singapore", 1, 0.28369, null, 0.05854, null, 0.97611, null, 0.92541, null, 30, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-12-24", "Undetermined", "Adult", "Liver", "Liver and Biliary System"], [37280, "SRR1057956", "SRX398514", "SRS518966", "SRP034710", "PRJNA232516", "Transcriptomic analyses of Kras induced zebrafish liver cancer", "GSE53630", "Transcriptome Analysis", "The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing  using three prime' RNA SAGE on SOLiD system", null, "pubmed:24633177", null, "6M1", "GSM1297512", null, "source name:control liver|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control", "6M1", "The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver", "one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", null, "tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control", "GSM1297512", "GSM1297512: 6M1; Danio rerio; RNA Seq", "GSM1297512", null, "1", "Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.", "GEO Accession:GSM1297512", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP034710", null, null, "6M1.csfasta.gz 6M1.qual.gz", "SOLiD_native SOLiD_native", 670343910.0, 22344797.0, "GSM1297512 r1", "0:30", "0:270812672;1:123662771;2:177982653;3:97335698;.:550116", 30, null, null, null, null, null, null, null, null, "SRX398514", "SRS518966", "SRA122333", "GEO", "National University of Singapore", 1, 0.28477, null, 0.05061, null, 0.9735, null, 0.86701, null, 30, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2013-12-24", "Undetermined", "Adult", "Liver", "Liver and Biliary System"], [38413, "SRR1821826", "SRX893427", "SRS859540", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver208 36m 3.75nM roten1 8w rep6", "GSM1620973", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks", "liver208 36m 3.75nM roten1 8w rep6", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks", "GSM1620973", "GSM1620973: liver208 36m 3.75nM roten1 8w rep6; Danio rerio; RNA Seq", "GSM1620973", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620973", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver208.fastq.gz", "fastq", 2200239850.0, 44004797.0, "GSM1620973 r1", "0:50", "A:571878023;C:528294946;G:516878213;T:582511055;N:677613", 50, null, null, null, 571878023, 528294946, 516878213, 582511055, 677613, "SRX893427", "SRS859540", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93543, null, 0.05381, null, 0.814, null, 0.56377, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38414, "SRR1821825", "SRX893426", "SRS859542", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver207 36m 3.75nM roten1 8w rep5", "GSM1620972", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks", "liver207 36m 3.75nM roten1 8w rep5", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks", "GSM1620972", "GSM1620972: liver207 36m 3.75nM roten1 8w rep5; Danio rerio; RNA Seq", "GSM1620972", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620972", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver207.fastq.gz", "fastq", 2434066300.0, 48681326.0, "GSM1620972 r1", "0:50", "A:647470716;C:574345677;G:559996925;T:651504881;N:748101", 50, null, null, null, 647470716, 574345677, 559996925, 651504881, 748101, "SRX893426", "SRS859542", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93196, null, 0.06713, null, 0.79916, null, 0.56304, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38415, "SRR1821824", "SRX893425", "SRS859544", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver206 36m 3.75nM roten1 8w rep4", "GSM1620971", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks", "liver206 36m 3.75nM roten1 8w rep4", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks", "GSM1620971", "GSM1620971: liver206 36m 3.75nM roten1 8w rep4; Danio rerio; RNA Seq", "GSM1620971", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620971", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver206.fastq.gz", "fastq", 2530671200.0, 50613424.0, "GSM1620971 r1", "0:50", "A:672377930;C:592838124;G:582426421;T:681213921;N:1814804", 50, null, null, null, 672377930, 592838124, 582426421, 681213921, 1814804, "SRX893425", "SRS859544", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93349, null, 0.0724, null, 0.7867, null, 0.56433, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38416, "SRR1821823", "SRX893424", "SRS859541", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver205 36m 3.75nM roten1 8w rep3", "GSM1620970", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks", "liver205 36m 3.75nM roten1 8w rep3", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks", "GSM1620970", "GSM1620970: liver205 36m 3.75nM roten1 8w rep3; Danio rerio; RNA Seq", "GSM1620970", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620970", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver205.fastq.gz", "fastq", 2149930050.0, 42998601.0, "GSM1620970 r1", "0:50", "A:568725900;C:507812500;G:497024054;T:576280556;N:87040", 50, null, null, null, 568725900, 507812500, 497024054, 576280556, 87040, "SRX893424", "SRS859541", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93606, null, 0.06193, null, 0.80012, null, 0.57505, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38417, "SRR1821822", "SRX893423", "SRS859543", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver204 36m 3.75nM roten1 8w rep2", "GSM1620969", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks", "liver204 36m 3.75nM roten1 8w rep2", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks", "GSM1620969", "GSM1620969: liver204 36m 3.75nM roten1 8w rep2; Danio rerio; RNA Seq", "GSM1620969", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620969", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver204.fastq.gz", "fastq", 2852874500.0, 57057490.0, "GSM1620969 r1", "0:50", "A:758952474;C:670213462;G:651059038;T:770418307;N:2231219", 50, null, null, null, 758952474, 670213462, 651059038, 770418307, 2231219, "SRX893423", "SRS859543", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92602, null, 0.0709, null, 0.78319, null, 0.55468, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38418, "SRR1821821", "SRX893422", "SRS859545", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver203 36m 3.75nM roten1 8w rep1", "GSM1620968", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks", "liver203 36m 3.75nM roten1 8w rep1", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:3.75nM roten1|duration:8 weeks", "GSM1620968", "GSM1620968: liver203 36m 3.75nM roten1 8w rep1; Danio rerio; RNA Seq", "GSM1620968", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620968", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver203.fastq.gz", "fastq", 2686262550.0, 53725251.0, "GSM1620968 r1", "0:50", "A:705831052;C:629469709;G:620794974;T:716919571;N:13247244", 50, null, null, null, 705831052, 629469709, 620794974, 716919571, 13247244, "SRX893422", "SRS859545", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.91348, null, 0.05511, null, 0.81347, null, 0.53272, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38419, "SRR1821820", "SRX893421", "SRS859546", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver172 36m 3.75nM roten1 3w rep4", "GSM1620967", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks", "liver172 36m 3.75nM roten1 3w rep4", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks", "GSM1620967", "GSM1620967: liver172 36m 3.75nM roten1 3w rep4; Danio rerio; RNA Seq", "GSM1620967", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620967", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver172.fastq.gz", "fastq", 2065136400.0, 41302728.0, "GSM1620967 r1", "0:50", "A:547988869;C:486083531;G:472243345;T:557154482;N:1666173", 50, null, null, null, 547988869, 486083531, 472243345, 557154482, 1666173, "SRX893421", "SRS859546", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92759, null, 0.0626, null, 0.79326, null, 0.52584, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38420, "SRR1821819", "SRX893420", "SRS859547", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver171 36m 3.75nM roten1 3w rep3", "GSM1620966", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks", "liver171 36m 3.75nM roten1 3w rep3", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks", "GSM1620966", "GSM1620966: liver171 36m 3.75nM roten1 3w rep3; Danio rerio; RNA Seq", "GSM1620966", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620966", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver171.fastq.gz", "fastq", 2410165800.0, 48203316.0, "GSM1620966 r1", "0:50", "A:638532163;C:560800416;G:550477924;T:648424639;N:11930658", 50, null, null, null, 638532163, 560800416, 550477924, 648424639, 11930658, "SRX893420", "SRS859547", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.9052, null, 0.07216, null, 0.77013, null, 0.54156, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38421, "SRR1821818", "SRX893419", "SRS859548", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver170 36m 3.75nM roten1 3w rep2", "GSM1620965", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks", "liver170 36m 3.75nM roten1 3w rep2", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks", "GSM1620965", "GSM1620965: liver170 36m 3.75nM roten1 3w rep2; Danio rerio; RNA Seq", "GSM1620965", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620965", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver170.fastq.gz", "fastq", 2077713200.0, 41554264.0, "GSM1620965 r1", "0:50", "A:547665152;C:493031219;G:478885586;T:558030382;N:100861", 50, null, null, null, 547665152, 493031219, 478885586, 558030382, 100861, "SRX893419", "SRS859548", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92951, null, 0.06604, null, 0.78813, null, 0.50562, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38422, "SRR1821817", "SRX893418", "SRS859549", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver168 36m 3.75nM roten1 3w rep1", "GSM1620964", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks", "liver168 36m 3.75nM roten1 3w rep1", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:3.75nM roten1|duration:3 weeks", "GSM1620964", "GSM1620964: liver168 36m 3.75nM roten1 3w rep1; Danio rerio; RNA Seq", "GSM1620964", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620964", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver168.fastq.gz", "fastq", 2043972800.0, 40879456.0, "GSM1620964 r1", "0:50", "A:537874539;C:485494677;G:472924858;T:547619633;N:59093", 50, null, null, null, 537874539, 485494677, 472924858, 547619633, 59093, "SRX893418", "SRS859549", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93165, null, 0.06093, null, 0.78443, null, 0.51626, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38423, "SRR1821816", "SRX893417", "SRS859550", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver188 36m control 8w rep3", "GSM1620963", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:n1|duration:8 weeks", "liver188 36m control 8w rep3", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:n1|duration:8 weeks", "GSM1620963", "GSM1620963: liver188 36m control 8w rep3; Danio rerio; RNA Seq", "GSM1620963", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620963", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver188.fastq.gz", "fastq", 2043860700.0, 40877214.0, "GSM1620963 r1", "0:50", "A:546509644;C:480578060;G:467994052;T:548137833;N:641111", 50, null, null, null, 546509644, 480578060, 467994052, 548137833, 641111, "SRX893417", "SRS859550", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.91484, null, 0.08158, null, 0.7559, null, 0.57112, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38424, "SRR1821815", "SRX893416", "SRS859551", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver186 36m control 8w rep2", "GSM1620962", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:n1|duration:8 weeks", "liver186 36m control 8w rep2", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:n1|duration:8 weeks", "GSM1620962", "GSM1620962: liver186 36m control 8w rep2; Danio rerio; RNA Seq", "GSM1620962", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620962", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver186.fastq.gz", "fastq", 1806504400.0, 36130088.0, "GSM1620962 r1", "0:50", "A:478503997;C:426614556;G:417975841;T:482136404;N:1273602", 50, null, null, null, 478503997, 426614556, 417975841, 482136404, 1273602, "SRX893416", "SRS859551", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93167, null, 0.06499, null, 0.79695, null, 0.53466, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38425, "SRR1821814", "SRX893415", "SRS859552", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver185 36m control 8w rep1", "GSM1620961", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:n1|duration:8 weeks", "liver185 36m control 8w rep1", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:n1|duration:8 weeks", "GSM1620961", "GSM1620961: liver185 36m control 8w rep1; Danio rerio; RNA Seq", "GSM1620961", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620961", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver185.fastq.gz", "fastq", 2656526050.0, 53130521.0, "GSM1620961 r1", "0:50", "A:700055044;C:626738929;G:622660107;T:706999824;N:72146", 50, null, null, null, 700055044, 626738929, 622660107, 706999824, 72146, "SRX893415", "SRS859552", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92972, null, 0.05926, null, 0.8001, null, 0.55293, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38426, "SRR1821813", "SRX893414", "SRS859555", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver162 36m control 3w rep2", "GSM1620960", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:n1|duration:3 weeks", "liver162 36m control 3w rep2", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:n1|duration:3 weeks", "GSM1620960", "GSM1620960: liver162 36m control 3w rep2; Danio rerio; RNA Seq", "GSM1620960", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620960", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver162.fastq.gz", "fastq", 2037943300.0, 40758866.0, "GSM1620960 r1", "0:50", "A:532287036;C:487343893;G:476293186;T:541912735;N:106450", 50, null, null, null, 532287036, 487343893, 476293186, 541912735, 106450, "SRX893414", "SRS859555", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92256, null, 0.05731, null, 0.79582, null, 0.52548, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38427, "SRR1821812", "SRX893413", "SRS859553", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver161 36m control 3w rep1", "GSM1620959", null, "source name:total RNA extracted from liver|tissue:liver|age:36 month|treatment:n1|duration:3 weeks", "liver161 36m control 3w rep1", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:36 month|treatment:n1|duration:3 weeks", "GSM1620959", "GSM1620959: liver161 36m control 3w rep1; Danio rerio; RNA Seq", "GSM1620959", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620959", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver161.fastq.gz", "fastq", 1931855350.0, 38637107.0, "GSM1620959 r1", "0:50", "A:506162541;C:457810984;G:450391101;T:513259108;N:4231616", 50, null, null, null, 506162541, 457810984, 450391101, 513259108, 4231616, "SRX893413", "SRS859553", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.91267, null, 0.06115, null, 0.78224, null, 0.54531, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38428, "SRR1821811", "SRX893412", "SRS859554", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver184 12m control 8w rep3", "GSM1620958", null, "source name:total RNA extracted from liver|tissue:liver|age:12 month|treatment:n1|duration:8 weeks", "liver184 12m control 8w rep3", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:12 month|treatment:n1|duration:8 weeks", "GSM1620958", "GSM1620958: liver184 12m control 8w rep3; Danio rerio; RNA Seq", "GSM1620958", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620958", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver184.fastq.gz", "fastq", 2612886200.0, 52257724.0, "GSM1620958 r1", "0:50", "A:692472911;C:614541298;G:602942228;T:702823776;N:105987", 50, null, null, null, 692472911, 614541298, 602942228, 702823776, 105987, "SRX893412", "SRS859554", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93487, null, 0.06068, null, 0.81237, null, 0.58828, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38429, "SRR1821810", "SRX893411", "SRS859556", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver183 12m control 8w rep2", "GSM1620957", null, "source name:total RNA extracted from liver|tissue:liver|age:12 month|treatment:n1|duration:8 weeks", "liver183 12m control 8w rep2", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:12 month|treatment:n1|duration:8 weeks", "GSM1620957", "GSM1620957: liver183 12m control 8w rep2; Danio rerio; RNA Seq", "GSM1620957", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620957", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver183.fastq.gz", "fastq", 3008273200.0, 60165464.0, "GSM1620957 r1", "0:50", "A:805204411;C:700890541;G:683878902;T:816000323;N:2299023", 50, null, null, null, 805204411, 700890541, 683878902, 816000323, 2299023, "SRX893411", "SRS859556", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.9234, null, 0.07513, null, 0.79884, null, 0.50199, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38430, "SRR1821809", "SRX893410", "SRS859559", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver182 12m control 8w rep1", "GSM1620956", null, "source name:total RNA extracted from liver|tissue:liver|age:12 month|treatment:n1|duration:8 weeks", "liver182 12m control 8w rep1", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:12 month|treatment:n1|duration:8 weeks", "GSM1620956", "GSM1620956: liver182 12m control 8w rep1; Danio rerio; RNA Seq", "GSM1620956", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620956", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver182.fastq.gz", "fastq", 2315532750.0, 46310655.0, "GSM1620956 r1", "0:50", "A:614278228;C:536988118;G:528915286;T:623991113;N:11360005", 50, null, null, null, 614278228, 536988118, 528915286, 623991113, 11360005, "SRX893410", "SRS859559", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.91729, null, 0.06968, null, 0.79778, null, 0.57634, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38431, "SRR1821808", "SRX893409", "SRS859557", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver159 12m control 3w rep2", "GSM1620955", null, "source name:total RNA extracted from liver|tissue:liver|age:12 month|treatment:n1|duration:3 weeks", "liver159 12m control 3w rep2", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:12 month|treatment:n1|duration:3 weeks", "GSM1620955", "GSM1620955: liver159 12m control 3w rep2; Danio rerio; RNA Seq", "GSM1620955", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620955", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver159.fastq.gz", "fastq", 1787795950.0, 35755919.0, "GSM1620955 r1", "0:50", "A:475365731;C:420351773;G:409097689;T:482893599;N:87158", 50, null, null, null, 475365731, 420351773, 409097689, 482893599, 87158, "SRX893409", "SRS859557", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92805, null, 0.07018, null, 0.7839, null, 0.57353, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [38432, "SRR1821807", "SRX893408", "SRS859558", "SRP055573", "PRJNA276667", "RNA seq of zebrafish brain  liver and skin during perturbation with rotenone at young and old age", "GSE66362", "Transcriptome Analysis", "Zebrafish of two different age groups 12 month and 36 month were treated with low amounts of rotenone mild stress and compared to untreated zebrafish. Two different durations were used 3 and 8 weeks. Illumina sequencing HiSeq2000 was applied to generate 50bp single end reads. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 68 sample: 3 tissues brain  liver  skin; 2 age groups 12 month and 36 month; controls and rotenone treated samples; 2 6 biological replicates for each group", null, "pubmed:27135165", null, "liver157 12m control 3w rep1", "GSM1620954", null, "source name:total RNA extracted from liver|tissue:liver|age:12 month|treatment:n1|duration:3 weeks", "liver157 12m control 3w rep1", "FASTQ files were extracted using Illumina Casava software v1.8.2.", "total RNA extracted from liver", "Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO control for 3 weeks and  8 weeks  respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "Zebrafish Danio rerio were raised under standard conditions.", "tissue:liver|age:12 month|treatment:n1|duration:3 weeks", "GSM1620954", "GSM1620954: liver157 12m control 3w rep1; Danio rerio; RNA Seq", "GSM1620954", null, "1", "Total RNA was isolated using QIAzol Qiagen  Hilden  Germany based on the phenol/chloroform extraction method. postwards the RNA was quantified photometrically with a NanoDrop 1000 PeqLab  Erlangen  Germany and stored at  80 \u00b0C until use. For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit Illumina; San Diego; CA  USA following the manufacturer's instruction.", "GEO Accession:GSM1620954", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP055573", null, null, "Liver157.fastq.gz", "fastq", 2375584950.0, 47511699.0, "GSM1620954 r1", "0:50", "A:636438966;C:553591776;G:539104775;T:646382105;N:67328", 50, null, null, null, 636438966, 553591776, 539104775, 646382105, 67328, "SRX893408", "SRS859558", "SRA244883", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.92658, null, 0.07029, null, 0.76359, null, 0.50995, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2015-02-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [39999, "SRR6081857", "SRX3220844", "SRS2545507", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 93+94", "GSM2795185", null, "source name:total RNA extracted from skin|strain:AB JxTu Tgwt1a:GFP|age:6 month|age category: |tissue:liver", "NH FLI liver 93+94", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgwt1a:GFP|age:6 month|age category: |tissue:liver", "GSM2795185", "GSM2795185: NH FLI liver 93+94; Danio rerio; RNA Seq", "GSM2795185", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM2795185", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_6m_DR93DR94.fq.gz", "fastq", 2333496400.0, 46669928.0, "GSM2795185 r1", "0:50", "A:614203790;C:555535741;G:543915663;T:619744641;N:96565", 50, null, null, null, 614203790, 555535741, 543915663, 619744641, 96565, "SRX3220844", "SRS2545507", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94566, null, 0.08285, null, 0.68876, null, 0.54555, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-09-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40000, "SRR6081856", "SRX3220843", "SRS2545506", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI skin 124", "GSM2795184", null, "source name:total RNA extracted from skin|strain:AB JxTu Tgwt1a:GFP|age:12 month|age category: |tissue:liver", "NH FLI skin 124", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from skin", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgwt1a:GFP|age:12 month|age category: |tissue:liver", "GSM2795184", "GSM2795184: NH FLI skin 124; Danio rerio; RNA Seq", "GSM2795184", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM2795184", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_12m_DR124.fq.gz", "fastq", 2804419350.0, 56088387.0, "GSM2795184 r1", "0:50", "A:727789828;C:665886619;G:674182975;T:736335760;N:224168", 50, null, null, null, 727789828, 665886619, 674182975, 736335760, 224168, "SRX3220843", "SRS2545506", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.96193, null, 0.04063, null, 0.7895, null, 0.23278, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-09-27", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40026, "SRR2751019", "SRX1362089", "SRS1125438", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 112", "GSM1915525", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver", "NH FLI liver 112", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver", "GSM1915525", "GSM1915525: NH FLI liver 112; Danio rerio; RNA Seq", "GSM1915525", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915525", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_42m_DR112.fq.gz", "fastq", 2493027200.0, 49860544.0, "GSM1915525 r1", "0:50", "A:655270619;C:590132953;G:584855596;T:662626178;N:141854", 50, null, null, null, 655270619, 590132953, 584855596, 662626178, 141854, "SRX1362089", "SRS1125438", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94015, null, 0.06186, null, 0.80777, null, 0.56276, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40027, "SRR2751018", "SRX1362088", "SRS1125437", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 110", "GSM1915524", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver", "NH FLI liver 110", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver", "GSM1915524", "GSM1915524: NH FLI liver 110; Danio rerio; RNA Seq", "GSM1915524", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915524", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_42m_DR110.fq.gz", "fastq", 2548926150.0, 50978523.0, "GSM1915524 r1", "0:50", "A:664677096;C:610795768;G:599120861;T:674104114;N:228311", 50, null, null, null, 664677096, 610795768, 599120861, 674104114, 228311, "SRX1362088", "SRS1125437", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.9507, null, 0.06053, null, 0.8127, null, 0.51968, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40028, "SRR2751017", "SRX1362087", "SRS1125440", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 109", "GSM1915523", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver", "NH FLI liver 109", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver", "GSM1915523", "GSM1915523: NH FLI liver 109; Danio rerio; RNA Seq", "GSM1915523", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915523", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_42m_DR109.fq.gz", "fastq", 2349260700.0, 46985214.0, "GSM1915523 r1", "0:50", "A:619110926;C:556823390;G:547569893;T:625605583;N:150908", 50, null, null, null, 619110926, 556823390, 547569893, 625605583, 150908, "SRX1362087", "SRS1125440", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94144, null, 0.06318, null, 0.76282, null, 0.57815, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40029, "SRR2751016", "SRX1362086", "SRS1125439", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 107", "GSM1915522", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver", "NH FLI liver 107", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver", "GSM1915522", "GSM1915522: NH FLI liver 107; Danio rerio; RNA Seq", "GSM1915522", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915522", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_42m_DR107.fq.gz", "fastq", 2819134200.0, 56382684.0, "GSM1915522 r1", "0:50", "A:739388911;C:669956842;G:658589434;T:750229539;N:969474", 50, null, null, null, 739388911, 669956842, 658589434, 750229539, 969474, "SRX1362086", "SRS1125439", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94944, null, 0.06329, null, 0.79433, null, 0.5582, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40030, "SRR2751015", "SRX1362085", "SRS1125441", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 106", "GSM1915521", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver", "NH FLI liver 106", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgwt1a:GFP|age:42 month|age category:old 2|tissue:liver", "GSM1915521", "GSM1915521: NH FLI liver 106; Danio rerio; RNA Seq", "GSM1915521", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915521", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_42m_DR106.fq.gz", "fastq", 2607094700.0, 52141894.0, "GSM1915521 r1", "0:50", "A:684681493;C:617936279;G:611124933;T:692780900;N:571095", 50, null, null, null, 684681493, 617936279, 611124933, 692780900, 571095, "SRX1362085", "SRS1125441", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94017, null, 0.06883, null, 0.77187, null, 0.53057, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40031, "SRR2751014", "SRX1362084", "SRS1125443", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 152", "GSM1915520", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver", "NH FLI liver 152", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver", "GSM1915520", "GSM1915520: NH FLI liver 152; Danio rerio; RNA Seq", "GSM1915520", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915520", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_36m_DR152.fq.gz", "fastq", 3427372500.0, 68547450.0, "GSM1915520 r1", "0:50", "A:878643380;C:836548343;G:816844380;T:894177988;N:1158409", 50, null, null, null, 878643380, 836548343, 816844380, 894177988, 1158409, "SRX1362084", "SRS1125443", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94444, null, 0.06122, null, 0.77875, null, 0.56481, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40032, "SRR2751013", "SRX1362083", "SRS1125442", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 151", "GSM1915519", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver", "NH FLI liver 151", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver", "GSM1915519", "GSM1915519: NH FLI liver 151; Danio rerio; RNA Seq", "GSM1915519", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915519", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_36m_DR151.fq.gz", "fastq", 2485583750.0, 49711675.0, "GSM1915519 r1", "0:50", "A:660843418;C:585986685;G:573818543;T:664714547;N:220557", 50, null, null, null, 660843418, 585986685, 573818543, 664714547, 220557, "SRX1362083", "SRS1125442", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93011, null, 0.08086, null, 0.7695, null, 0.5595, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40033, "SRR2751012", "SRX1362082", "SRS1125444", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 150", "GSM1915518", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver", "NH FLI liver 150", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver", "GSM1915518", "GSM1915518: NH FLI liver 150; Danio rerio; RNA Seq", "GSM1915518", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915518", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_36m_DR150.fq.gz", "fastq", 2519190600.0, 50383812.0, "GSM1915518 r1", "0:50", "A:655881049;C:600722119;G:600690081;T:661791601;N:105750", 50, null, null, null, 655881049, 600722119, 600690081, 661791601, 105750, "SRX1362082", "SRS1125444", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94575, null, 0.05521, null, 0.82333, null, 0.58307, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40034, "SRR2751011", "SRX1362081", "SRS1125446", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 147", "GSM1915517", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver", "NH FLI liver 147", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver", "GSM1915517", "GSM1915517: NH FLI liver 147; Danio rerio; RNA Seq", "GSM1915517", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915517", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_36m_DR147.fq.gz", "fastq", 2259586100.0, 45191722.0, "GSM1915517 r1", "0:50", "A:598439339;C:531150489;G:524393660;T:605396290;N:206322", 50, null, null, null, 598439339, 531150489, 524393660, 605396290, 206322, "SRX1362081", "SRS1125446", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93951, null, 0.05741, null, 0.82063, null, 0.5414, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40035, "SRR2751010", "SRX1362080", "SRS1125413", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 146", "GSM1915516", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver", "NH FLI liver 146", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgpu.1:GFP|age:36 month|age category:old 1|tissue:liver", "GSM1915516", "GSM1915516: NH FLI liver 146; Danio rerio; RNA Seq", "GSM1915516", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915516", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_36m_DR146.fq.gz", "fastq", 2286592350.0, 45731847.0, "GSM1915516 r1", "0:50", "A:575985495;C:563341201;G:554727838;T:592210592;N:327224", 50, null, null, null, 575985495, 563341201, 554727838, 592210592, 327224, "SRX1362080", "SRS1125413", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94558, null, 0.05047, null, 0.7904, null, 0.56079, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40036, "SRR2751009", "SRX1362079", "SRS1125409", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 138", "GSM1915515", null, "source name:total RNA extracted from liver|strain:AB JxTu|age:24 month|age category: |tissue:liver", "NH FLI liver 138", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu|age:24 month|age category: |tissue:liver", "GSM1915515", "GSM1915515: NH FLI liver 138; Danio rerio; RNA Seq", "GSM1915515", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915515", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_24m_DR138.fq.gz", "fastq", 3843216450.0, 76864329.0, "GSM1915515 r1", "0:50", "A:1018176854;C:908623218;G:891363243;T:1024377821;N:675314", 50, null, null, null, 1018176854, 908623218, 891363243, 1024377821, 675314, "SRX1362079", "SRS1125409", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.9442, null, 0.06874, null, 0.76264, null, 0.52537, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40037, "SRR2751008", "SRX1362078", "SRS1125408", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 136", "GSM1915514", null, "source name:total RNA extracted from liver|strain:AB JxTu|age:24 month|age category: |tissue:liver", "NH FLI liver 136", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu|age:24 month|age category: |tissue:liver", "GSM1915514", "GSM1915514: NH FLI liver 136; Danio rerio; RNA Seq", "GSM1915514", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915514", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_24m_DR136.fq.gz", "fastq", 3668583250.0, 73371665.0, "GSM1915514 r1", "0:50", "A:961648869;C:879998251;G:866556900;T:960048700;N:330530", 50, null, null, null, 961648869, 879998251, 866556900, 960048700, 330530, "SRX1362078", "SRS1125408", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93746, null, 0.06166, null, 0.80389, null, 0.52831, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40038, "SRR2751007", "SRX1362077", "SRS1125445", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 135", "GSM1915513", null, "source name:total RNA extracted from liver|strain:AB JxTu|age:24 month|age category: |tissue:liver", "NH FLI liver 135", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu|age:24 month|age category: |tissue:liver", "GSM1915513", "GSM1915513: NH FLI liver 135; Danio rerio; RNA Seq", "GSM1915513", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915513", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_24m_DR135.fq.gz", "fastq", 2511261600.0, 50225232.0, "GSM1915513 r1", "0:50", "A:668637105;C:587542062;G:579925851;T:674944365;N:212217", 50, null, null, null, 668637105, 587542062, 579925851, 674944365, 212217, "SRX1362077", "SRS1125445", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.9436, null, 0.09452, null, 0.76958, null, 0.54588, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40039, "SRR2751006", "SRX1362076", "SRS1125447", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 134", "GSM1915512", null, "source name:total RNA extracted from liver|strain:AB JxTu|age:24 month|age category: |tissue:liver", "NH FLI liver 134", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu|age:24 month|age category: |tissue:liver", "GSM1915512", "GSM1915512: NH FLI liver 134; Danio rerio; RNA Seq", "GSM1915512", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915512", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_24m_DR134.fq.gz", "fastq", 2496794600.0, 49935892.0, "GSM1915512 r1", "0:50", "A:657127337;C:591970066;G:582273775;T:664995064;N:428358", 50, null, null, null, 657127337, 591970066, 582273775, 664995064, 428358, "SRX1362076", "SRS1125447", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94435, null, 0.06912, null, 0.78354, null, 0.54526, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40040, "SRR2751005", "SRX1362075", "SRS1125410", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 133", "GSM1915511", null, "source name:total RNA extracted from liver|strain:AB JxTu|age:24 month|age category: |tissue:liver", "NH FLI liver 133", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu|age:24 month|age category: |tissue:liver", "GSM1915511", "GSM1915511: NH FLI liver 133; Danio rerio; RNA Seq", "GSM1915511", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915511", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_24m_DR133.fq.gz", "fastq", 2364294900.0, 47285898.0, "GSM1915511 r1", "0:50", "A:621349333;C:562020902;G:553860502;T:626647310;N:416853", 50, null, null, null, 621349333, 562020902, 553860502, 626647310, 416853, "SRX1362075", "SRS1125410", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94368, null, 0.07791, null, 0.73198, null, 0.53494, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40041, "SRR2751004", "SRX1362074", "SRS1125448", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 126", "GSM1915510", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver", "NH FLI liver 126", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver", "GSM1915510", "GSM1915510: NH FLI liver 126; Danio rerio; RNA Seq", "GSM1915510", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915510", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_12m_DR126.fq.gz", "fastq", 2614833700.0, 52296674.0, "GSM1915510 r1", "0:50", "A:676534455;C:632762889;G:618276106;T:686974287;N:285963", 50, null, null, null, 676534455, 632762889, 618276106, 686974287, 285963, "SRX1362074", "SRS1125448", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95004, null, 0.04888, null, 0.82544, null, 0.56527, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40042, "SRR2751003", "SRX1362073", "SRS1125449", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 125", "GSM1915509", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver", "NH FLI liver 125", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver", "GSM1915509", "GSM1915509: NH FLI liver 125; Danio rerio; RNA Seq", "GSM1915509", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915509", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_12m_DR125.fq.gz", "fastq", 2263792150.0, 45275843.0, "GSM1915509 r1", "0:50", "A:595799795;C:537810224;G:528914425;T:601165834;N:101872", 50, null, null, null, 595799795, 537810224, 528914425, 601165834, 101872, "SRX1362073", "SRS1125449", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94421, null, 0.06353, null, 0.79028, null, 0.57064, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40043, "SRR2751002", "SRX1362072", "SRS1125451", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 122", "GSM1915508", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver", "NH FLI liver 122", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver", "GSM1915508", "GSM1915508: NH FLI liver 122; Danio rerio; RNA Seq", "GSM1915508", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915508", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_12m_DR122.fq.gz", "fastq", 2275428550.0, 45508571.0, "GSM1915508 r1", "0:50", "A:594149425;C:543561508;G:537246828;T:600158700;N:312089", 50, null, null, null, 594149425, 543561508, 537246828, 600158700, 312089, "SRX1362072", "SRS1125451", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94529, null, 0.06272, null, 0.7722, null, 0.55271, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40044, "SRR2751001", "SRX1362071", "SRS1125450", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 120", "GSM1915507", null, "source name:total RNA extracted from liver|strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver", "NH FLI liver 120", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu Tgflk:mCherry|age:12 month|age category: |tissue:liver", "GSM1915507", "GSM1915507: NH FLI liver 120; Danio rerio; RNA Seq", "GSM1915507", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915507", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_12m_DR120.fq.gz", "fastq", 2265086750.0, 45301735.0, "GSM1915507 r1", "0:50", "A:601521692;C:533720206;G:522717695;T:606780756;N:346401", 50, null, null, null, 601521692, 533720206, 522717695, 606780756, 346401, "SRX1362071", "SRS1125450", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93885, null, 0.08013, null, 0.76221, null, 0.58231, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40045, "SRR2751000", "SRX1362070", "SRS1125452", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 98", "GSM1915506", null, "source name:total RNA extracted from liver|strain:AB JxTu|age:6 month|age category:young|tissue:liver", "NH FLI liver 98", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu|age:6 month|age category:young|tissue:liver", "GSM1915506", "GSM1915506: NH FLI liver 98; Danio rerio; RNA Seq", "GSM1915506", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915506", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_6m_DR98.fq.gz", "fastq", 2776070850.0, 55521417.0, "GSM1915506 r1", "0:50", "A:728235383;C:663729749;G:645210407;T:738761794;N:133517", 50, null, null, null, 728235383, 663729749, 645210407, 738761794, 133517, "SRX1362070", "SRS1125452", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94666, null, 0.05668, null, 0.82759, null, 0.56255, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40046, "SRR2750999", "SRX1362069", "SRS1125453", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 96", "GSM1915505", null, "source name:total RNA extracted from liver|strain:AB JxTu|age:6 month|age category:young|tissue:liver", "NH FLI liver 96", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu|age:6 month|age category:young|tissue:liver", "GSM1915505", "GSM1915505: NH FLI liver 96; Danio rerio; RNA Seq", "GSM1915505", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915505", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_6m_DR96.fq.gz", "fastq", 2726829450.0, 54536589.0, "GSM1915505 r1", "0:50", "A:718243835;C:648108983;G:635655237;T:724565315;N:256080", 50, null, null, null, 718243835, 648108983, 635655237, 724565315, 256080, "SRX1362069", "SRS1125453", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94101, null, 0.06016, null, 0.81972, null, 0.5434, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40047, "SRR2750998", "SRX1362068", "SRS1125458", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 86", "GSM1915504", null, "source name:total RNA extracted from liver|strain:AB JxTu|age:6 month|age category:young|tissue:liver", "NH FLI liver 86", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu|age:6 month|age category:young|tissue:liver", "GSM1915504", "GSM1915504: NH FLI liver 86; Danio rerio; RNA Seq", "GSM1915504", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915504", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_6m_DR86.fq.gz", "fastq", 2321789450.0, 46435789.0, "GSM1915504 r1", "0:50", "A:621943405;C:541049700;G:532136200;T:626281665;N:378480", 50, null, null, null, 621943405, 541049700, 532136200, 626281665, 378480, "SRX1362068", "SRS1125458", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94025, null, 0.08134, null, 0.76775, null, 0.56079, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40048, "SRR2750997", "SRX1362067", "SRS1125454", "SRP065208", "PRJNA299585", "Deep sequencing of mRNA from Danio rerio at five different timepoints in three different tissues brain  liver  skin", "GSE74244", "Transcriptome Analysis", "Comparison of temporal gene expression profiles Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 75 samples in sum; 5 age groups 6  12  24  36  42 month; 3 tissues brain  liver  skin; 5 samples per group", null, "pubmed:29382830", null, "NH FLI liver 85", "GSM1915503", null, "source name:total RNA extracted from liver|strain:AB JxTu|age:6 month|age category:young|tissue:liver", "NH FLI liver 85", "Illumina Casava v1.8.0 software used for extraction of FASTQ files Reads were mapped using Tophat v2.0.6 to the genome taken the annotation into account:  tophat2  p 24  o OUTPUTDIR  g 1   no coverage search   transcriptome index=transcriptome data/Danio rerio.Zv9.73 Danio rerio.Zv9.73 Counting of reads per gene was done using htseq count: htseq count   quiet   stranded=no   idattr=gene id   mode=union SAMFILE Danio rerio.Zv9.73.gtf > OUTPUTFILE Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Gene were excluded from dataset if at least one sample has a RPKM of 0. Genome build: Ensemble Zv9.73 Supplementary files format and content: Excel file includes raw counts and RPKM values for each sample", "total RNA extracted from liver", null, "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", null, "strain:AB JxTu|age:6 month|age category:young|tissue:liver", "GSM1915503", "GSM1915503: NH FLI liver 85; Danio rerio; RNA Seq", "GSM1915503", null, "1", "Total RNA from was extracted as described Baumgart et al.  2012; PMID:22487494 Preparation of libraries was done using Illumina\u2019s TruSeq RNA sample prep kit following the manufacturer\u2019s instruction.", "GEO Accession:GSM1915503", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP065208", null, null, "liver_6m_DR85.fq.gz", "fastq", 2153807800.0, 43076156.0, "GSM1915503 r1", "0:50", "A:577891421;C:502278275;G:490571575;T:582818284;N:248245", 50, null, null, null, 577891421, 502278275, 490571575, 582818284, 248245, "SRX1362067", "SRS1125454", "SRA306458", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93585, null, 0.08978, null, 0.75365, null, 0.56334, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2015-10-21", "Adult", "Adult", "Liver", "Liver and Biliary System"], [40743, "SRR3342393", "SRX1684659", "SRS1379870", "SRP072957", "PRJNA317597", "FOXN3 regulates hepatic glucose utilization", "GSE80003", "Transcriptome Analysis", "We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 in the liver and non transgenic siblings Overall design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings", null, "pubmed:27292639", null, "Transgenic3", "GSM2109873", null, "source name:foxn3 overexpression liver|tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae", "Transgenic3", "Reads were aligned to the genome using novoalign Annotated splice junctions generated by the MakeTranscriptome command in the USeq Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq Differential gene expression analysis was performed on the resulting count table using DESeq2 Genome build: Zv9 genome build Supplementary files format and content: excel file with read counts  FPKM and statistical analysis", "foxn3 overexpression liver", null, "Total RNA\u00a0 extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine", null, "tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae", "GSM2109873", "GSM2109873: Transgenic3; Danio rerio; RNA Seq", "GSM2109873", null, "1", "Total RNA\u00a0 extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine", "GEO Accession:GSM2109873", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP072957", null, null, "11405X8_150225_D00294_0165_AC6BKMANXX_7.txt.gz", "fastq", 1538486450.0, 30769729.0, "GSM2109873 r1", "0:50", "A:399631224;C:339577730;G:345815787;T:453436273;N:25436", 50, null, null, null, 399631224, 339577730, 345815787, 453436273, 25436, "SRX1684659", "SRS1379870", "SRA405566", "GEO", "Amnon Schlegel, Molecular Medicine Program, University of Utah School of Medicine", 1, 0.89036, null, 0.28368, null, 0.75461, null, 0.63309, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-06", "Larval", "Larval", "Liver", "Liver and Biliary System"], [40744, "SRR3342392", "SRX1684658", "SRS1379871", "SRP072957", "PRJNA317597", "FOXN3 regulates hepatic glucose utilization", "GSE80003", "Transcriptome Analysis", "We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 in the liver and non transgenic siblings Overall design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings", null, "pubmed:27292639", null, "Transgenic2", "GSM2109872", null, "source name:foxn3 overexpression liver|tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae", "Transgenic2", "Reads were aligned to the genome using novoalign Annotated splice junctions generated by the MakeTranscriptome command in the USeq Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq Differential gene expression analysis was performed on the resulting count table using DESeq2 Genome build: Zv9 genome build Supplementary files format and content: excel file with read counts  FPKM and statistical analysis", "foxn3 overexpression liver", null, "Total RNA\u00a0 extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine", null, "tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae", "GSM2109872", "GSM2109872: Transgenic2; Danio rerio; RNA Seq", "GSM2109872", null, "1", "Total RNA\u00a0 extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine", "GEO Accession:GSM2109872", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP072957", null, null, "11405X7_150225_D00294_0165_AC6BKMANXX_7.txt.gz", "fastq", 1500971700.0, 30019434.0, "GSM2109872 r1", "0:50", "A:389353802;C:331408746;G:327481397;T:452703447;N:24308", 50, null, null, null, 389353802, 331408746, 327481397, 452703447, 24308, "SRX1684658", "SRS1379871", "SRA405566", "GEO", "Amnon Schlegel, Molecular Medicine Program, University of Utah School of Medicine", 1, 0.9148, null, 0.242, null, 0.76784, null, 0.44492, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-06", "Larval", "Larval", "Liver", "Liver and Biliary System"], [40745, "SRR3342391", "SRX1684657", "SRS1379872", "SRP072957", "PRJNA317597", "FOXN3 regulates hepatic glucose utilization", "GSE80003", "Transcriptome Analysis", "We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 in the liver and non transgenic siblings Overall design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings", null, "pubmed:27292639", null, "Transgenic1", "GSM2109871", null, "source name:foxn3 overexpression liver|tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae", "Transgenic1", "Reads were aligned to the genome using novoalign Annotated splice junctions generated by the MakeTranscriptome command in the USeq Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq Differential gene expression analysis was performed on the resulting count table using DESeq2 Genome build: Zv9 genome build Supplementary files format and content: excel file with read counts  FPKM and statistical analysis", "foxn3 overexpression liver", null, "Total RNA\u00a0 extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine", null, "tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae", "GSM2109871", "GSM2109871: Transgenic1; Danio rerio; RNA Seq", "GSM2109871", null, "1", "Total RNA\u00a0 extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine", "GEO Accession:GSM2109871", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP072957", null, null, "11405X6_150225_D00294_0165_AC6BKMANXX_7.txt.gz", "fastq", 1672645200.0, 33452904.0, "GSM2109871 r1", "0:50", "A:446934700;C:363616773;G:354194568;T:507871249;N:27910", 50, null, null, null, 446934700, 363616773, 354194568, 507871249, 27910, "SRX1684657", "SRS1379872", "SRA405566", "GEO", "Amnon Schlegel, Molecular Medicine Program, University of Utah School of Medicine", 1, 0.90431, null, 0.33357, null, 0.75075, null, 0.62394, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-06", "Larval", "Larval", "Liver", "Liver and Biliary System"], [40746, "SRR3342390", "SRX1684656", "SRS1379873", "SRP072957", "PRJNA317597", "FOXN3 regulates hepatic glucose utilization", "GSE80003", "Transcriptome Analysis", "We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 in the liver and non transgenic siblings Overall design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings", null, "pubmed:27292639", null, "WT3", "GSM2109870", null, "source name:wildtype liver|tissue:Liver|developmental stage:7 dpf larvae", "WT3", "Reads were aligned to the genome using novoalign Annotated splice junctions generated by the MakeTranscriptome command in the USeq Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq Differential gene expression analysis was performed on the resulting count table using DESeq2 Genome build: Zv9 genome build Supplementary files format and content: excel file with read counts  FPKM and statistical analysis", "wildtype liver", null, "Total RNA\u00a0 extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine", null, "tissue:Liver|developmental stage:7 dpf larvae", "GSM2109870", "GSM2109870: WT3; Danio rerio; RNA Seq", "GSM2109870", null, "1", "Total RNA\u00a0 extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine", "GEO Accession:GSM2109870", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP072957", null, null, "11405X4_150225_D00294_0165_AC6BKMANXX_7.txt.gz", "fastq", 1621245550.0, 32424911.0, "GSM2109870 r1", "0:50", "A:387275594;C:392477306;G:410916447;T:430550072;N:26131", 50, null, null, null, 387275594, 392477306, 410916447, 430550072, 26131, "SRX1684656", "SRS1379873", "SRA405566", "GEO", "Amnon Schlegel, Molecular Medicine Program, University of Utah School of Medicine", 1, 0.75787, null, 0.22112, null, 0.80858, null, 0.6379, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-06", "Larval", "Larval", "Liver", "Liver and Biliary System"], [40747, "SRR3342389", "SRX1684655", "SRS1379874", "SRP072957", "PRJNA317597", "FOXN3 regulates hepatic glucose utilization", "GSE80003", "Transcriptome Analysis", "We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 in the liver and non transgenic siblings Overall design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings", null, "pubmed:27292639", null, "WT2", "GSM2109869", null, "source name:wildtype liver|tissue:Liver|developmental stage:7 dpf larvae", "WT2", "Reads were aligned to the genome using novoalign Annotated splice junctions generated by the MakeTranscriptome command in the USeq Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq Differential gene expression analysis was performed on the resulting count table using DESeq2 Genome build: Zv9 genome build Supplementary files format and content: excel file with read counts  FPKM and statistical analysis", "wildtype liver", null, "Total RNA\u00a0 extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine", null, "tissue:Liver|developmental stage:7 dpf larvae", "GSM2109869", "GSM2109869: WT2; Danio rerio; RNA Seq", "GSM2109869", null, "1", "Total RNA\u00a0 extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine", "GEO Accession:GSM2109869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP072957", null, null, "11405X3_150225_D00294_0165_AC6BKMANXX_7.txt.gz", "fastq", 1660295850.0, 33205917.0, "GSM2109869 r1", "0:50", "A:441731711;C:362842137;G:351944677;T:503749546;N:27779", 50, null, null, null, 441731711, 362842137, 351944677, 503749546, 27779, "SRX1684655", "SRS1379874", "SRA405566", "GEO", "Amnon Schlegel, Molecular Medicine Program, University of Utah School of Medicine", 1, 0.90993, null, 0.31148, null, 0.74602, null, 0.62587, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-06", "Larval", "Larval", "Liver", "Liver and Biliary System"], [40748, "SRR3342388", "SRX1684654", "SRS1379875", "SRP072957", "PRJNA317597", "FOXN3 regulates hepatic glucose utilization", "GSE80003", "Transcriptome Analysis", "We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 in the liver and non transgenic siblings Overall design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings", null, "pubmed:27292639", null, "WT1", "GSM2109868", null, "source name:wildtype liver|tissue:Liver|developmental stage:7 dpf larvae", "WT1", "Reads were aligned to the genome using novoalign Annotated splice junctions generated by the MakeTranscriptome command in the USeq Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq Differential gene expression analysis was performed on the resulting count table using DESeq2 Genome build: Zv9 genome build Supplementary files format and content: excel file with read counts  FPKM and statistical analysis", "wildtype liver", null, "Total RNA\u00a0 extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine", null, "tissue:Liver|developmental stage:7 dpf larvae", "GSM2109868", "GSM2109868: WT1; Danio rerio; RNA Seq", "GSM2109868", null, "1", "Total RNA\u00a0 extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine", "GEO Accession:GSM2109868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP072957", null, null, "11405X2_150225_D00294_0165_AC6BKMANXX_7.txt.gz", "fastq", 1588346650.0, 31766933.0, "GSM2109868 r1", "0:50", "A:427469407;C:345629775;G:329846628;T:485374945;N:25895", 50, null, null, null, 427469407, 345629775, 329846628, 485374945, 25895, "SRX1684654", "SRS1379875", "SRA405566", "GEO", "Amnon Schlegel, Molecular Medicine Program, University of Utah School of Medicine", 1, 0.89836, null, 0.33182, null, 0.75694, null, 0.62202, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-04-06", "Larval", "Larval", "Liver", "Liver and Biliary System"], [41669, "SRR5119946", "SRX2435221", "SRS1870216", "SRP095327", "PRJNA358007", "Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer", "GSE92544", "Transcriptome Analysis", "Liver cancer is a common cause of cancer death  with a male predominant incidence due  in part  to increased estrogen levels in cirrhotic patients. It is unknown  however  how estrogen is sensed to influence this process. Here  we show that estrogen activates the G protein coupled estrogen receptor 1 GPER1  expressed in hepatocytes  to enhancing hepatocyte size  cell cycle progression and cell proliferation  thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling  and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis  specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth  mTOR activation  and can serve as a therapeutic target for liver cancer treatment. Overall design: RNA Seq analysis of control DMSO treated livers and \u00df Estradiol exposed livers were examined.", null, "pubmed:30641053", null, "GC24 WT Female E2 3", "GSM2432117", null, "source name:liver  \u03b2 Estradiol|tissue:liver|developmental stage:adult|genotype:Wild type", "GC24 WT Female E2 3", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: danRer7 Supplementary files format and content: excel files include RPKM values for each Sample", "liver  \u03b2 Estradiol", "Zebrafish were raised until at 3 mpf Fish were then treated daily with DMSO or \u03b2 Estradiol for a period of 6 weeks.", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines IACUC. At 3 mpf  a selected group of wild type male and female zebrafish were seperated into individual tanks to control food consumption.", "tissue:liver|developmental stage:adult|genotype:Wild type", "GSM2432117", "GSM2432117: GC24 WT Female E2 3; Danio rerio; RNA Seq", "GSM2432117", null, "1", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "GEO Accession:GSM2432117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP095327", null, null, "GC24_WT_Female_3_E2_R1_.final.fastq.gz", "fastq", 2351822445.0, 31180880.0, "GSM2432117 r1", "0:75.43 1:0", "A:606315394;C:550835503;G:552007320;T:642535245;N:128983", 75, 0, null, null, 606315394, 550835503, 552007320, 642535245, 128983, "SRX2435221", "SRS1870216", "SRA505252", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.95886, null, 0.04527, null, 0.82881, null, 0.25455, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Adult", "Adult", "Liver", "Liver and Biliary System"], [41670, "SRR5119945", "SRX2435220", "SRS1870215", "SRP095327", "PRJNA358007", "Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer", "GSE92544", "Transcriptome Analysis", "Liver cancer is a common cause of cancer death  with a male predominant incidence due  in part  to increased estrogen levels in cirrhotic patients. It is unknown  however  how estrogen is sensed to influence this process. Here  we show that estrogen activates the G protein coupled estrogen receptor 1 GPER1  expressed in hepatocytes  to enhancing hepatocyte size  cell cycle progression and cell proliferation  thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling  and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis  specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth  mTOR activation  and can serve as a therapeutic target for liver cancer treatment. Overall design: RNA Seq analysis of control DMSO treated livers and \u00df Estradiol exposed livers were examined.", null, "pubmed:30641053", null, "GC23 WT Female E2 2", "GSM2432116", null, "source name:liver  \u03b2 Estradiol|tissue:liver|developmental stage:adult|genotype:Wild type", "GC23 WT Female E2 2", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: danRer7 Supplementary files format and content: excel files include RPKM values for each Sample", "liver  \u03b2 Estradiol", "Zebrafish were raised until at 3 mpf Fish were then treated daily with DMSO or \u03b2 Estradiol for a period of 6 weeks.", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines IACUC. At 3 mpf  a selected group of wild type male and female zebrafish were seperated into individual tanks to control food consumption.", "tissue:liver|developmental stage:adult|genotype:Wild type", "GSM2432116", "GSM2432116: GC23 WT Female E2 2; Danio rerio; RNA Seq", "GSM2432116", null, "1", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "GEO Accession:GSM2432116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP095327", null, null, "GC23_WT_Female_2_E2_R1_.final.fastq.gz", "fastq", 2432965856.0, 32507869.0, "GSM2432116 r1", "0:74.84 1:0", "A:640756461;C:566459908;G:555884156;T:664022500;N:5842831", 74, 0, null, null, 640756461, 566459908, 555884156, 664022500, 5842831, "SRX2435220", "SRS1870215", "SRA505252", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.95687, null, 0.04516, null, 0.83788, null, 0.24521, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Adult", "Adult", "Liver", "Liver and Biliary System"], [41671, "SRR5119944", "SRX2435219", "SRS1870217", "SRP095327", "PRJNA358007", "Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer", "GSE92544", "Transcriptome Analysis", "Liver cancer is a common cause of cancer death  with a male predominant incidence due  in part  to increased estrogen levels in cirrhotic patients. It is unknown  however  how estrogen is sensed to influence this process. Here  we show that estrogen activates the G protein coupled estrogen receptor 1 GPER1  expressed in hepatocytes  to enhancing hepatocyte size  cell cycle progression and cell proliferation  thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling  and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis  specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth  mTOR activation  and can serve as a therapeutic target for liver cancer treatment. Overall design: RNA Seq analysis of control DMSO treated livers and \u00df Estradiol exposed livers were examined.", null, "pubmed:30641053", null, "GC22 WT Female E2 1", "GSM2432115", null, "source name:liver  \u03b2 Estradiol|tissue:liver|developmental stage:adult|genotype:Wild type", "GC22 WT Female E2 1", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: danRer7 Supplementary files format and content: excel files include RPKM values for each Sample", "liver  \u03b2 Estradiol", "Zebrafish were raised until at 3 mpf Fish were then treated daily with DMSO or \u03b2 Estradiol for a period of 6 weeks.", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines IACUC. At 3 mpf  a selected group of wild type male and female zebrafish were seperated into individual tanks to control food consumption.", "tissue:liver|developmental stage:adult|genotype:Wild type", "GSM2432115", "GSM2432115: GC22 WT Female E2 1; Danio rerio; RNA Seq", "GSM2432115", null, "1", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "GEO Accession:GSM2432115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP095327", null, null, "GC22_WT_Female_1_E2_R1_.final.fastq.gz", "fastq", 1514848138.0, 20065836.0, "GSM2432115 r1", "0:75.49 1:0", "A:401143638;C:350293240;G:337536196;T:425842580;N:32484", 75, 0, null, null, 401143638, 350293240, 337536196, 425842580, 32484, "SRX2435219", "SRS1870217", "SRA505252", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.92886, null, 0.03089, null, 0.8255, null, 0.3351, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Adult", "Adult", "Liver", "Liver and Biliary System"], [41672, "SRR5119943", "SRX2435218", "SRS1870214", "SRP095327", "PRJNA358007", "Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer", "GSE92544", "Transcriptome Analysis", "Liver cancer is a common cause of cancer death  with a male predominant incidence due  in part  to increased estrogen levels in cirrhotic patients. It is unknown  however  how estrogen is sensed to influence this process. Here  we show that estrogen activates the G protein coupled estrogen receptor 1 GPER1  expressed in hepatocytes  to enhancing hepatocyte size  cell cycle progression and cell proliferation  thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling  and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis  specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth  mTOR activation  and can serve as a therapeutic target for liver cancer treatment. Overall design: RNA Seq analysis of control DMSO treated livers and \u00df Estradiol exposed livers were examined.", null, "pubmed:30641053", null, "GC21 WT Male E2 3", "GSM2432114", null, "source name:liver  \u03b2 Estradiol|tissue:liver|developmental stage:adult|genotype:Wild type", "GC21 WT Male E2 3", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: danRer7 Supplementary files format and content: excel files include RPKM values for each Sample", "liver  \u03b2 Estradiol", "Zebrafish were raised until at 3 mpf Fish were then treated daily with DMSO or \u03b2 Estradiol for a period of 6 weeks.", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines IACUC. At 3 mpf  a selected group of wild type male and female zebrafish were seperated into individual tanks to control food consumption.", "tissue:liver|developmental stage:adult|genotype:Wild type", "GSM2432114", "GSM2432114: GC21 WT Male E2 3; Danio rerio; RNA Seq", "GSM2432114", null, "1", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "GEO Accession:GSM2432114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP095327", null, null, "GC21_WT_Male_3_E2_R1_.final.fastq.gz", "fastq", 1755929959.0, 23259158.0, "GSM2432114 r1", "0:75.49 1:0", "A:448892515;C:410588213;G:410376465;T:486059421;N:13345", 75, 0, null, null, 448892515, 410588213, 410376465, 486059421, 13345, "SRX2435218", "SRS1870214", "SRA505252", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.96848, null, 0.03334, null, 0.83167, null, 0.21006, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Adult", "Adult", "Liver", "Liver and Biliary System"], [41673, "SRR5119942", "SRX2435217", "SRS1870213", "SRP095327", "PRJNA358007", "Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer", "GSE92544", "Transcriptome Analysis", "Liver cancer is a common cause of cancer death  with a male predominant incidence due  in part  to increased estrogen levels in cirrhotic patients. It is unknown  however  how estrogen is sensed to influence this process. Here  we show that estrogen activates the G protein coupled estrogen receptor 1 GPER1  expressed in hepatocytes  to enhancing hepatocyte size  cell cycle progression and cell proliferation  thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling  and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis  specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth  mTOR activation  and can serve as a therapeutic target for liver cancer treatment. Overall design: RNA Seq analysis of control DMSO treated livers and \u00df Estradiol exposed livers were examined.", null, "pubmed:30641053", null, "GC20 WT Male E2 2", "GSM2432113", null, "source name:liver  \u03b2 Estradiol|tissue:liver|developmental stage:adult|genotype:Wild type", "GC20 WT Male E2 2", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: danRer7 Supplementary files format and content: excel files include RPKM values for each Sample", "liver  \u03b2 Estradiol", "Zebrafish were raised until at 3 mpf Fish were then treated daily with DMSO or \u03b2 Estradiol for a period of 6 weeks.", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines IACUC. At 3 mpf  a selected group of wild type male and female zebrafish were seperated into individual tanks to control food consumption.", "tissue:liver|developmental stage:adult|genotype:Wild type", "GSM2432113", "GSM2432113: GC20 WT Male E2 2; Danio rerio; RNA Seq", "GSM2432113", null, "1", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "GEO Accession:GSM2432113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP095327", null, null, "GC20_WT_Male_2_E2_R1_.final.fastq.gz", "fastq", 1716932758.0, 22757647.0, "GSM2432113 r1", "0:75.44 1:0", "A:438799191;C:399722209;G:404593734;T:473746439;N:71185", 75, 0, null, null, 438799191, 399722209, 404593734, 473746439, 71185, "SRX2435217", "SRS1870213", "SRA505252", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.96898, null, 0.044, null, 0.86149, null, 0.2305, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Adult", "Adult", "Liver", "Liver and Biliary System"], [41674, "SRR5119941", "SRX2435216", "SRS1870212", "SRP095327", "PRJNA358007", "Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer", "GSE92544", "Transcriptome Analysis", "Liver cancer is a common cause of cancer death  with a male predominant incidence due  in part  to increased estrogen levels in cirrhotic patients. It is unknown  however  how estrogen is sensed to influence this process. Here  we show that estrogen activates the G protein coupled estrogen receptor 1 GPER1  expressed in hepatocytes  to enhancing hepatocyte size  cell cycle progression and cell proliferation  thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling  and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis  specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth  mTOR activation  and can serve as a therapeutic target for liver cancer treatment. Overall design: RNA Seq analysis of control DMSO treated livers and \u00df Estradiol exposed livers were examined.", null, "pubmed:30641053", null, "GC19 WT Male E2 1", "GSM2432112", null, "source name:liver  \u03b2 Estradiol|tissue:liver|developmental stage:adult|genotype:Wild type", "GC19 WT Male E2 1", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: danRer7 Supplementary files format and content: excel files include RPKM values for each Sample", "liver  \u03b2 Estradiol", "Zebrafish were raised until at 3 mpf Fish were then treated daily with DMSO or \u03b2 Estradiol for a period of 6 weeks.", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines IACUC. At 3 mpf  a selected group of wild type male and female zebrafish were seperated into individual tanks to control food consumption.", "tissue:liver|developmental stage:adult|genotype:Wild type", "GSM2432112", "GSM2432112: GC19 WT Male E2 1; Danio rerio; RNA Seq", "GSM2432112", null, "1", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "GEO Accession:GSM2432112", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP095327", null, null, "GC19_WT_Male_1_E2_R1_.final.fastq.gz", "fastq", 1733319813.0, 22973322.0, "GSM2432112 r1", "0:75.45 1:0", "A:443874461;C:411280496;G:411171660;T:466944592;N:48604", 75, 0, null, null, 443874461, 411280496, 411171660, 466944592, 48604, "SRX2435216", "SRS1870212", "SRA505252", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.95987, null, 0.03426, null, 0.77005, null, 0.34825, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Adult", "Adult", "Liver", "Liver and Biliary System"], [41675, "SRR5119940", "SRX2435215", "SRS1870211", "SRP095327", "PRJNA358007", "Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer", "GSE92544", "Transcriptome Analysis", "Liver cancer is a common cause of cancer death  with a male predominant incidence due  in part  to increased estrogen levels in cirrhotic patients. It is unknown  however  how estrogen is sensed to influence this process. Here  we show that estrogen activates the G protein coupled estrogen receptor 1 GPER1  expressed in hepatocytes  to enhancing hepatocyte size  cell cycle progression and cell proliferation  thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling  and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis  specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth  mTOR activation  and can serve as a therapeutic target for liver cancer treatment. Overall design: RNA Seq analysis of control DMSO treated livers and \u00df Estradiol exposed livers were examined.", null, "pubmed:30641053", null, "GC12 WT Female 3", "GSM2432111", null, "source name:liver  DMSO|tissue:liver|developmental stage:adult|genotype:Wild type", "GC12 WT Female 3", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: danRer7 Supplementary files format and content: excel files include RPKM values for each Sample", "liver  DMSO", "Zebrafish were raised until at 3 mpf Fish were then treated daily with DMSO or \u03b2 Estradiol for a period of 6 weeks.", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines IACUC. At 3 mpf  a selected group of wild type male and female zebrafish were seperated into individual tanks to control food consumption.", "tissue:liver|developmental stage:adult|genotype:Wild type", "GSM2432111", "GSM2432111: GC12 WT Female 3; Danio rerio; RNA Seq", "GSM2432111", null, "1", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "GEO Accession:GSM2432111", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP095327", null, null, "GC12_WT_Female_3_R1_.final.fastq.gz", "fastq", 2284787283.0, 30379215.0, "GSM2432111 r1", "0:75.21 1:0", "A:584159482;C:532290526;G:535767276;T:630438326;N:2131673", 75, 0, null, null, 584159482, 532290526, 535767276, 630438326, 2131673, "SRX2435215", "SRS1870211", "SRA505252", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.9725, null, 0.03468, null, 0.87578, null, 0.19476, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Adult", "Adult", "Liver", "Liver and Biliary System"], [41676, "SRR5119939", "SRX2435214", "SRS1870210", "SRP095327", "PRJNA358007", "Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer", "GSE92544", "Transcriptome Analysis", "Liver cancer is a common cause of cancer death  with a male predominant incidence due  in part  to increased estrogen levels in cirrhotic patients. It is unknown  however  how estrogen is sensed to influence this process. Here  we show that estrogen activates the G protein coupled estrogen receptor 1 GPER1  expressed in hepatocytes  to enhancing hepatocyte size  cell cycle progression and cell proliferation  thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling  and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis  specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth  mTOR activation  and can serve as a therapeutic target for liver cancer treatment. Overall design: RNA Seq analysis of control DMSO treated livers and \u00df Estradiol exposed livers were examined.", null, "pubmed:30641053", null, "GC11 WT Female 2", "GSM2432110", null, "source name:liver  DMSO|tissue:liver|developmental stage:adult|genotype:Wild type", "GC11 WT Female 2", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: danRer7 Supplementary files format and content: excel files include RPKM values for each Sample", "liver  DMSO", "Zebrafish were raised until at 3 mpf Fish were then treated daily with DMSO or \u03b2 Estradiol for a period of 6 weeks.", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines IACUC. 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For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "GEO Accession:GSM2432110", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP095327", null, null, "GC11_WT_Female_2_R1_.final.fastq.gz", "fastq", 1491973497.0, 19763630.0, "GSM2432110 r1", "0:75.49 1:0", "A:382261682;C:348981942;G:346075046;T:414634100;N:20727", 75, 0, null, null, 382261682, 348981942, 346075046, 414634100, 20727, "SRX2435214", "SRS1870210", "SRA505252", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.97078, null, 0.0383, null, 0.84411, null, 0.25595, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Adult", "Adult", "Liver", "Liver and Biliary System"], [41677, "SRR5119938", "SRX2435213", "SRS1870209", "SRP095327", "PRJNA358007", "Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer", "GSE92544", "Transcriptome Analysis", "Liver cancer is a common cause of cancer death  with a male predominant incidence due  in part  to increased estrogen levels in cirrhotic patients. It is unknown  however  how estrogen is sensed to influence this process. Here  we show that estrogen activates the G protein coupled estrogen receptor 1 GPER1  expressed in hepatocytes  to enhancing hepatocyte size  cell cycle progression and cell proliferation  thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling  and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis  specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth  mTOR activation  and can serve as a therapeutic target for liver cancer treatment. Overall design: RNA Seq analysis of control DMSO treated livers and \u00df Estradiol exposed livers were examined.", null, "pubmed:30641053", null, "GC10 WT Female 1", "GSM2432109", null, "source name:liver  DMSO|tissue:liver|developmental stage:adult|genotype:Wild type", "GC10 WT Female 1", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: danRer7 Supplementary files format and content: excel files include RPKM values for each Sample", "liver  DMSO", "Zebrafish were raised until at 3 mpf Fish were then treated daily with DMSO or \u03b2 Estradiol for a period of 6 weeks.", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines IACUC. At 3 mpf  a selected group of wild type male and female zebrafish were seperated into individual tanks to control food consumption.", "tissue:liver|developmental stage:adult|genotype:Wild type", "GSM2432109", "GSM2432109: GC10 WT Female 1; Danio rerio; RNA Seq", "GSM2432109", null, "1", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "GEO Accession:GSM2432109", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP095327", null, null, "GC10_WT_Female_1_R1_.final.fastq.gz", "fastq", 1585437627.0, 21103252.0, "GSM2432109 r1", "0:75.13 1:0", "A:406380540;C:367144383;G:372462566;T:437518788;N:1931350", 75, 0, null, null, 406380540, 367144383, 372462566, 437518788, 1931350, "SRX2435213", "SRS1870209", "SRA505252", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.97478, null, 0.03048, null, 0.87677, null, 0.16476, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Adult", "Adult", "Liver", "Liver and Biliary System"], [41678, "SRR5119937", "SRX2435212", "SRS1870208", "SRP095327", "PRJNA358007", "Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer", "GSE92544", "Transcriptome Analysis", "Liver cancer is a common cause of cancer death  with a male predominant incidence due  in part  to increased estrogen levels in cirrhotic patients. It is unknown  however  how estrogen is sensed to influence this process. Here  we show that estrogen activates the G protein coupled estrogen receptor 1 GPER1  expressed in hepatocytes  to enhancing hepatocyte size  cell cycle progression and cell proliferation  thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling  and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis  specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth  mTOR activation  and can serve as a therapeutic target for liver cancer treatment. Overall design: RNA Seq analysis of control DMSO treated livers and \u00df Estradiol exposed livers were examined.", null, "pubmed:30641053", null, "GC9 WT Male 3", "GSM2432108", null, "source name:liver  DMSO|tissue:liver|developmental stage:adult|genotype:Wild type", "GC9 WT Male 3", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: danRer7 Supplementary files format and content: excel files include RPKM values for each Sample", "liver  DMSO", "Zebrafish were raised until at 3 mpf Fish were then treated daily with DMSO or \u03b2 Estradiol for a period of 6 weeks.", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines IACUC. At 3 mpf  a selected group of wild type male and female zebrafish were seperated into individual tanks to control food consumption.", "tissue:liver|developmental stage:adult|genotype:Wild type", "GSM2432108", "GSM2432108: GC9 WT Male 3; Danio rerio; RNA Seq", "GSM2432108", null, "1", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "GEO Accession:GSM2432108", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP095327", null, null, "GC9_WT_Male_3_R1_.final.fastq.gz", "fastq", 1512010654.0, 20022544.0, "GSM2432108 r1", "0:75.52 1:0", "A:384125071;C:357935858;G:341294088;T:428626442;N:29195", 75, 0, null, null, 384125071, 357935858, 341294088, 428626442, 29195, "SRX2435212", "SRS1870208", "SRA505252", "GEO", "Oncology/Hematology, Boston Children's Hospital", 1, 0.95739, null, 0.06355, null, 0.82146, null, 0.54213, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Adult", "Adult", "Liver", "Liver and Biliary System"], [41679, "SRR5119936", "SRX2435211", "SRS1870207", "SRP095327", "PRJNA358007", "Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer", "GSE92544", "Transcriptome Analysis", "Liver cancer is a common cause of cancer death  with a male predominant incidence due  in part  to increased estrogen levels in cirrhotic patients. It is unknown  however  how estrogen is sensed to influence this process. Here  we show that estrogen activates the G protein coupled estrogen receptor 1 GPER1  expressed in hepatocytes  to enhancing hepatocyte size  cell cycle progression and cell proliferation  thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling  and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis  specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth  mTOR activation  and can serve as a therapeutic target for liver cancer treatment. Overall design: RNA Seq analysis of control DMSO treated livers and \u00df Estradiol exposed livers were examined.", null, "pubmed:30641053", null, "GC8 WT Male 2", "GSM2432107", null, "source name:liver  DMSO|tissue:liver|developmental stage:adult|genotype:Wild type", "GC8 WT Male 2", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: danRer7 Supplementary files format and content: excel files include RPKM values for each Sample", "liver  DMSO", "Zebrafish were raised until at 3 mpf Fish were then treated daily with DMSO or \u03b2 Estradiol for a period of 6 weeks.", "Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies  isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction  NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol", "All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines IACUC. 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"columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_layout\" = :p0 and \"experiment.library_selection\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "cDNA", "p2": "Liver"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 378, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 378, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver", "results": [{"value": "cDNA", "label": "cDNA", "count": 378, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Liver", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 378, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=cDNA&tissue_curation=Liver", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 347, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&experiment.platform=ILLUMINA", "selected": false}, {"value": "ABI_SOLID", "label": "ABI_SOLID", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&experiment.platform=ABI_SOLID", "selected": false}, {"value": "PACBIO_SMRT", "label": "PACBIO_SMRT", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&experiment.platform=PACBIO_SMRT", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver", "results": [{"value": "Adult", "label": "Adult", "count": 208, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&devstage_curation_coarse=Adult", "selected": false}, {"value": "Larval", "label": "Larval", "count": 70, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&devstage_curation_coarse=Larval", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 69, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&devstage_curation_coarse=Undetermined", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 31, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&devstage_curation_coarse=Multi-stage", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver", "results": [{"value": "Adult", "label": "Adult", "count": 194, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&devstage_curation=Adult", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 115, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&devstage_curation=Undetermined", "selected": false}, {"value": "Larval", "label": "Larval", "count": 38, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&devstage_curation=Larval", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 31, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&devstage_curation=Multi-stage", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver", "results": [{"value": "Liver and Biliary System", "label": "Liver and Biliary System", "count": 378, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&tissue_curation_coarse=Liver+and+Biliary+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver", "results": [{"value": "Liver", "label": "Liver", "count": 378, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver", "results": [{"value": "unknown", "label": "unknown", "count": 363, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&technology=unknown", "selected": false}, {"value": "bulk", "label": "bulk", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&technology=bulk", "selected": false}, {"value": "smartseq", "label": "smartseq", "count": 7, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&technology=smartseq", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "41679", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=cDNA&tissue_curation=Liver&_next=41679", "private": false, "allow_execute_sql": true, "query_ms": 176.7971109948121}